EP2319941A2 - Procédé et appareil pour corréler des niveaux de produits biomarqueurs avec une maladie - Google Patents

Procédé et appareil pour corréler des niveaux de produits biomarqueurs avec une maladie Download PDF

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EP2319941A2
EP2319941A2 EP11150414A EP11150414A EP2319941A2 EP 2319941 A2 EP2319941 A2 EP 2319941A2 EP 11150414 A EP11150414 A EP 11150414A EP 11150414 A EP11150414 A EP 11150414A EP 2319941 A2 EP2319941 A2 EP 2319941A2
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gene
rna
blood
genes
mrna
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EP2319941A3 (fr
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StageZero Life Sciences Ltd
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    • C12Q2600/00—Oligonucleotides characterized by their use
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Definitions

  • the disclosure relates to, apparatus and kits and computer based methods for correlating data corresponding to levels of biomarker products with a disease state in a subject.
  • Colorectal cancer is the second-leading cause of cancer-related deaths in the United States (11). Each year, approximately 150,000 people are diagnosed with colorectal cancer and almost 60,000 people die from the disease. Of those diagnosed, nearly half are expected to die within five years, since most cancers are detected when the cancer is less treatable. For those whose cancer is detected at an earlier stage, the five-year survival rate can be greater than 90%.
  • the American Cancer Society recommends that all Americans age 50 and older be screened regularly for colorectal cancer. Unfortunately, only a fraction of this population is screened for the disease, as currently available screening technologies are considered as either too costly, and/or too invasive or in some cases insufficiently accurate.
  • the inventions described herein identify biomarkers not previously associated with colorectal pathology whose gene expression levels, measured alone or in combination, and optionally applied to formulas to convert the levels to a measure, give an indication of a likelihood of colorectal pathology.
  • kits comprising packaging and containing one or more primer sets, wherein each set of which is able to generate an amplification product by selective amplification of at least a portion of a polynucleotide complementary to one or more RNA products of a biomarker, wherein the biomarker is a gene selected from the group consisting of: BCNP1, CD163, CDA, MS4A1, BANK1, and MCG20553; and wherein each set of the primer sets is selective for a different biomarker.
  • the complementary polynucleotide is selected from the group consisting of total RNA, mRNA, DNA, cDNA and EST.
  • the one or more biomarkers are at least two biomarkers.
  • the kit further comprises two or more components selected from the group consisting of: a thermostable polymerase, a reverse transcriptase, deoxynucleotide triphosphates, nucleotide triphosphates and enzyme buffer.
  • ascertaining whether the data characterizes either: (i) subjects having the one or more colorectal pathologies, or (ii) subjects not having the one or more colorectal pathologies comprises applying to the data a formula based on (i) a dataset representing levels of one or more products of each of the biomarkers in each subject of a reference population having the one or more pathologies, and (ii) a dataset representing levels of one or more products of each of the biomarkers in each subject of a reference population not having the one or more pathologies.
  • each isolated polynucleotide selectively hybridizes to (a) an RNA product of a biomarker selected from the group consisting of membrane-bound transcription factor protease site 1 (MBTPS1); MGC45871; muskelin 1 (MKLN1); nipped-B homolog (NIPBL); acylpeptide hydrolase (APEH); FLJ23091; MGC40157; and protein phosphatase 1 regulatory subunit 2 (PPP1R2); and/or (b) a polynucleotide sequence complementary to (a), wherein the composition is used to measure the level of RNA expression of at least two of the biomarkers.
  • a biomarker selected from the group consisting of membrane-bound transcription factor protease site 1 (MBTPS1); MGC45871; muskelin 1 (MKLN1); nipped-B homolog (NIPBL); acylpeptide hydrolase (APEH); FLJ23091; MGC40157; and protein
  • composition comprising a collection of two or more sets of biomarker specific primers as set out in Table 4 and/or Table 6.
  • normal refers to an individual or group of individuals who do not have colorectal pathology
  • diagnosis of said individual or group of individuals not having colorectal pathology is determined using conventional diagnostic methods.
  • said individual or group of individuals have not been diagnosed with any other disease.
  • Normal also refers to samples isolated from normal individuals and includes blood, total RNA or mRNA isolated from normal individuals. A sample taken from a normal individual can include a sample taken from an individual who does not have colorectal pathology at the time the sample is taken.
  • fusion protein refers to a polypeptide that comprises an amino acid sequence of a first protein or polypeptide or functional fragment, analog or derivative thereof, and an amino acid sequence of a heterologous protein, polypeptide, or peptide (i.e., a second protein or polypeptide or fragment, analog or derivative thereof different than the first protein or fragment, analog or derivative thereof).
  • a fusion protein comprises a prophylactic or therapeutic agent fused to a heterologous protein, polypeptide or peptide.
  • the heterologous protein, polypeptide or peptide may or may not be a different type of prophylactic or therapeutic agent.
  • hybridizing to or “hybridization” refers to the sequence specific non-covalent binding interactions with a complementary nucleic acid, for example interactions between a target nucleic acid sequence and a nucleic acid member on an array.
  • a first therapy e.g., a first prophylactic or therapeutic agent
  • a first prophylactic or therapeutic agent can be administered prior to (e.g., 5 minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks before), concommitantly with, or subsequent to (e.g., 5 minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks after) the administration of a second therapy (e.g., a second prophylactic or therapeutic agent) to a subject.
  • a second therapy e.g., a second prophylactic or therapeutic agent
  • a sample which is "isolated and/or derived” includes a sample which has been removed it from its natural environment in a subject and also includes samples which are further modified or altered.
  • samples can include tissue, lymph, bodily fluid, blood, RNA, protein, mRNA, serum reduced blood, erythrocyte reduced blood, serum reduced and erythrocyte reduced blood, unfractionated cells of a lysed blood, globin reduced mRNA, cDNA, PCR products and the like.
  • the level of expression when referring to RNA can also refer to a measurable quantity of a given nucleic acid as determined relative to the amount of total RNA, or cDNA used in QRT-PCR wherein the amount of total RNA used is 100ng; 50ng, 25ng; 10ng; 5ng; 1.25ng; 0.05ng; 0.3ng; 0.1ng; 0.09 ng; 0.08ng; 0.07ng; 0.06ng; or 0.05ng.
  • the level of expression of a nucleic acid can be determined by any methods known in the art. For microarray analysis, the level of expression is measured by hybridization analysis using nucleic acids corresponding to RNA isolated from one or more individuals according to methods well known in the art.
  • the antibody can be an intact immunoglobulin, e.g., an IgA, IgG, IgE, IgD, IgM or subtypes thereof.
  • the antibody can be conjugated to a functional moiety (e.g., a compound which has a biological or chemical function (which may be a second different polypeptide, a therapeutic drug, a cytotoxic agent, a detectable moiety, or a support.
  • a polypeptide ligand e.g. antibody of the invention interacts with a polypeptide, encoded by one of the genes of a biomarker, with high affinity and specificity.
  • mRNA means an RNA complementary to a gene; an mRNA includes a protein coding region, and also may include 5' end and 3' untranslated regions (UTR).
  • mRNA integrity refers to the quality of mRNA extracts from either tissue samples or samples.
  • mRNA extracts with good integrity do not appear to be degraded when examined by methods well known in the art, for example, by RNA agarose gel electrophoresis (e.g., Ausubel et al., John Wiley & Sons, Inc., 1997, Currant Protocols in Molecular Biology ).
  • the mRNA samples have good integrity (e.g., less than 10%, in some embodiments less than 5%, and more in some embodiments less than 1% of the mRNA is degraded) to truly represent the gene expression levels of sample from which they are extracted.
  • the acids that can be used to prepare pharmaceutically acceptable acid addition salts of such basic compounds are those that form non-toxic acid addition salts, i.e., salts containing pharmacologically acceptable anions, including but not limited to sulfuric, citric, maleic, acetic, oxalic, hydrochloride, hydrobromide, hydroiodide, nitrate, sulfate, bisulfate, phosphate, acid phosphate, isonicotinate, acetate, lactate, salicylate, citrate, acid citrate, tartrate, oleate, tannate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonate and pam
  • Compounds that include an amino moiety may form pharmaceutically acceptable salts with various amino acids, in addition to the acids mentioned above.
  • Compounds that are acidic in nature are capable of forming base salts with various pharmacologically acceptable cations.
  • Examples of such salts include alkali metal or alkaline earth metal salts and, particularly, calcium, magnesium, sodium lithium, zinc, potassium, and iron salts.
  • the backbone of the polynucleotide can comprise sugars and phosphate groups, as may typically be found in RNA or DNA, or modified or substituted sugar or phosphate groups.
  • a polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs.
  • the sequence of nucleotides may be interrupted by non-nucleotide components.
  • proteinaceous agent refers to polypeptides, proteins, peptides, and the like.
  • biomarker specific set of primers or “primer sets” as used herein refers to a set of polynucleotide primers wherein one primer primes the synthesis of a sense strand, and the second primer primes the synthesis of an antisense strand so as to produce double stranded DNA complementary to a portion of one or more RNA products of the biomarker of the invention.
  • a biomarker specific set of primers can be selected so that they will selectively amplify only portions of a polynucleotide complementary to one or more RNA products of a biomarker and do not amplify portions of polynucleotides complementary to other biomarkers.
  • analogs of oligomers may be polymers in which the sugar moiety has been modified or replaced by another suitable moiety, resulting in polymers which include, but are not limited to, morpholino analogs and peptide nucleic acid (PNA) analogs ( Egholm, et al. Peptide Nucleic Acids (PNA)--Oligonucleotide Analogues with an Achiral Peptide Backbone, (1992 )).
  • PNA peptide nucleic acid
  • Probes may also be mixtures of any of the oligonucleotide analog types together or in combination with native DNA or RNA and may also include linker species. At the same time, the oligonucleotides and analogs thereof may be used alone or in combination with one or more additional oligonucleotides or analogs thereof.
  • the term "products of the biomarker” or “biomarker products” refers to a species of RNA or a species of protein (wherein a species of RNA or protein can include multiple copies) isolated and/or derived from a sample including a tissue sample, a lymph sample, a lymph tissue sample, or a blood sample, or a fraction of a blood sample which corresponds to the biomarker (i.e., is transcribed from the gene or genetic element or is translated from RNA which is transcribed from the gene or genetic element). See Table 3 and Table 13.
  • the RNA may be pre-mRNA, mRNA, spliced variants of mRNA and the like.
  • the protein may be in its native state or post-translationally processed in any one of various ways.
  • the "reference population” or “test population” refers to one or more populations of "control samples" used to develop one or more classifier.
  • a single reference population can be divided into subpopulations.
  • two or more reference populations can be used.
  • a classifier can be developed to differentiate between individuals with one or more colorectal pathologies or one or more polyps or one or more subtypes of polyps and individuals without the same colorectal pathology or one or more polyps or one or more subtypes of polyps.
  • a first reference population would be comprised of individuals with the one or more colorectal pathologies and a second reference population would be comprised of individuals without the one or more colorectal pathologies.
  • the "reference population” or “test population” can be comprised of control samples from a number of individuals diagnosed with one or more colorectal pathologies including one or more polyps or one or more subtypes of polyps and individuals not having the colorectal pathologies or not having the one or more polyps or not having the one or more subtypes of polyps as determined using conventional diagnostic techniques.
  • the population of individuals having one or more colorectal pathologies can be selected to include individuals having a single subtype of polyp or one or more subtypes of polyps.
  • the individuals who do not have one or more colon pathologies can include individuals who have been diagnosed with other disease or diseases.
  • the individuals who do not have one or more colon pathologies can include individuals who have been diagnosed with other cancers.
  • the "reference population” or "test population” is comprised of a roughly equivalent number of "control samples" from each trait subgroup (e.g., in this instance wherein said trait is a determination of status with regards to the presence of colorectal pathology).
  • each trait subgroup (e.g. having or not having colorectal pathology) of the "reference population” has a similar distribution with regards to other traits e.g., age, sex, drug status, etc.
  • specific hybridizes can refer to hybridization which occurs when two nucleic acid sequences are substantially complementary (at least about 65% complementary over a stretch of at least 14 to 25 nucleotides, preferably at least about 75% complementary, more preferably at least about 90% complementary). See Kanehisa, M., 1984, Nucleic acids Res., 12:203 , incorporated herein by reference. As a result, it is expected that a certain degree of mismatch is tolerated. Such mismatch may be small, such as a mono-, di- or tri-nucleotide.
  • the support is glass. In some embodiments, at least one surface of the substrate will be substantially flat. In some embodiments, the support will contain reactive groups, including, but not limited to, carboxyl, amino, hydroxyl, thiol, and the like. In one embodiment, the support is optically transparent.
  • the term "synergistic” refers to a combination of a compound identified using one of the methods described herein, and another therapy (e.g., agent), which is more effective than the additive effects of the therapies.
  • another therapy e.g., agent
  • such other therapy has been or is currently being to prevent, treat, or ameliorate one or more colorectal pathologies including one or more polyps or one or more subtypes of polyps.
  • a synergistic effect of a combination of therapies permits the use of lower dosages of one or more of the therapies and/or less frequent administration of said therapies to an individual with colorectal pathologies including polyps or subtypes of polyps.
  • a “therapeutic agent” or “agent” refers to a compound that increases or decreases the expression of a polynucleotide or polypeptide sequences that are differentially expressed in a sample from an individual having one or more colorectal pathologies including polyps or a subtype of polyps.
  • the invention provides for a "therapeutic agent” that 1) prevents the formation of colorectal pathology 2) reduces, delays, or eliminates advancement or transformation of colorectal pathology and/or 3) restores one or more expression profiles of one or more colorectal pathology indicative nucleic acids or polypeptides of a patient to a profile more similar to that of a normal individual when administered to a patient.
  • the term "therapeutically effective amount” refers to that amount of a therapy (e.g., a therapeutic agent) sufficient to treat one or more colorectal pathologies including polyps or one or more subtypes of polyps; prevent one or more colorectal pathologies including polyps or one or more subtypes of polyps; prevent colorectal pathologies including polyps or one or more subtypes of polyps from transforming and/or advancing to colorectal cancer, cause regression of colorectal pathology, polyps or one or more subtypes of polyps, or to enhance or improve the therapeutic effect(s) of another therapy (e.g., therapeutic agent).
  • a therapy e.g., a therapeutic agent
  • a therapeutically effective amount refers to the amount of a therapy (e.g., a therapeutic agent) that modulates gene expression of the products of the biomarkers of the inventions.
  • a therapeutically effective amount of a therapy e.g., a therapeutic agent modulates gene expression of the products of the biomarkers of the invention at least 5%, preferably at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 100% relative to a control therapeutic agent such as phosphate buffered saline ("PBS").
  • PBS phosphate buffered saline
  • Samples for use in the invention include refers to any one of various type of molecules, cells and/or tissues which can be isolated and/or derived from a test subject and/or control subject, and which contains one or more biomarker products.
  • the sample can be isolated and/or derived from any fluid, cell or tissue.
  • the sample can also be one which is isolated and/or derived from any fluid and/or tissue which predominantly comprises blood cells.
  • the sample which is isolated and/or derived from an individual can be assayed for gene expression products, particularly genes expression products differentially expressed in individuals with or without one or more colorectal pathologies.
  • the sample is a fluid sample, a lymph sample, a lymph tissue sample or a blood sample.
  • the sample is isolated and/or derived from peripheral blood.
  • the sample may be isolated and/or derived from alternate sources, including ,from any one of various types of lymphoid tissue.
  • a sample of blood is obtained from an individual according to methods well known in the art.
  • a sample of blood may be obtained from an individual, for example a subject having one or more colorectal pathologies, suspected of having one or more colorectal pathologies or not having one or more colorectal pathologies.
  • a drop of blood is collected from a simple pin prick made in the skin of an individual.
  • Blood may be drawn from an individual from any part of the body (e.g., a finger, a hand, a wrist, an arm, a leg, a foot, an ankle, a stomach, and a neck) using techniques known to one of skill in the art, in particular methods of phlebotomy known in the art.
  • 0.001 ml, 0.005 ml, 0.01 ml, 0.05 ml, 0.1 ml, 0.15 ml, 0.2 ml, 0.25 ml, 0.5 ml, 0.75 ml, 1 ml, 1.5 ml, 2 ml, 3 ml, 4 ml, 5 ml, 10 ml, 15 ml or more of blood is collected from a subject.
  • 0.001 ml to 15m1 0.01 ml to 10 ml, 0.1 ml to 10 ml, 0.1 ml to 5 ml, 1 to 5 ml of blood is collected from an individual.
  • 0.001-100ml, preferably 0.01-50ml, more preferably 0.01-25ml and most preferably 0.01-1ml of blood is collected from an individual.
  • blood cells are separated from whole blood collected from an individual using other techniques known in the art.
  • blood collected from an individual can be subjected to Ficoll-Hypaque (Pharmacia) gradient centrifugation.
  • Ficoll-Hypaque gradient centrifugation is useful to isolate peripheral blood leukocytes (PBLs) which can be used in accordance with the methods of the invention.
  • macrophages can be obtained as follows. Mononuclear cells are isolated from peripheral blood of a subject, by syringe removal of blood followed by Ficoll-Hypaque gradient centrifugation. Tissue culture dishes are pre-coated with the subject's own serum or with AB+ human serum and incubated at 37°C for one hour. Non-adherent cells are removed by pipetting. Cold (4°C) 1mM EDTA in phosphate-buffered saline is added to the adherent cells left in the dish and the dishes are left at room temperature for fifteen minutes. The cells are harvested, washed with RPMI buffer and suspended in RPMI buffer.
  • Increased numbers of macrophages can be obtained by incubating at 37°C with macrophage-colony stimulating factor (M-CSF).
  • M-CSF macrophage-colony stimulating factor
  • Antibodies against macrophage specific surface markers, such as Mac-1 can be labeled by conjugation of an affinity compound to such molecules to facilitate detection and separation of macrophages.
  • Affinity compounds that can be used include but are not limited to biotin, photobiotin, fluorescein isothiocyante (FITC), or phycoerythrin (PE), or other compounds known in the art.
  • Cells retaining labeled antibodies are then separated from cells that do not bind such antibodies by techniques known in the art such as, but not limited to, various cell sorting methods, affinity chromatography, and panning.
  • the cells are incubated with the fluorescently labeled antibody or ligand for a time period sufficient to allow the labeled antibody or ligand to bind to cells.
  • the cells are processed through the cell sorter, allowing separation of the cells of interest from other cells. FACS sorted particles can be directly deposited into individual wells of microtiter plates to facilitate separation.
  • Magnetic beads can be also used to separate blood cells in some embodiments of the present invention.
  • blood cells can be sorted using a using a magnetic activated cell sorting (MACS) technique, a method for separating particles based on their ability to bind magnetic beads (0.5-100 m diameter).
  • a variety of useful modifications can be performed on the magnetic microspheres, including covalent addition of an antibody which specifically recognizes a cell-solid phase surface molecule or hapten.
  • a magnetic field is then applied, to physically manipulate the selected beads.
  • antibodies to a blood cell surface marker are coupled to magnetic beads.
  • the beads are then mixed with the blood cell culture to allow binding. Cells are then passed through a magnetic field to separate out cells having the blood cell surface markers of interest. These cells can then be isolated.
  • the surface of a culture dish may be coated with antibodies, and used to separate blood cells by a method called panning. Separate dishes can be coated with antibody specific to particular blood cells. Cells can be added first to a dish coated with blood cell specific antibodies of interest. After thorough rinsing, the cells left bound to the dish will be cells that express the blood cell markers of interest.
  • RNA is prepared by first collecting blood into a PAXgeneTM collection tube and then subsequently isolating the RNA using the PAXgeneTM blood RNA isolated system provided by PreAnalytiX, a Qiagen/BD company.
  • RNA is prepared by first collecting blood into any known stabilizing soluation (e.g. a PAXgeneTM collection or a TEMPUS® collection tube and then isolating the RNA using any method known to a person skilled in the art.
  • RNA is isolated first and then is subsequently treated to remove globin mRNA using one of any technique known in the art. For example, one can hybridize DNA primers and/or probes specific for globin RNA and utilize RNAse H to selectively degrade globin mRNA. In other embodiments RNA is isolated in a manner which removes the globin RNA during the RNA isolation steps (for example reducing globin RNA by selectively removing globin RNA using globin primers and/or probes attached to paramagnetic particles).
  • RNA integrity is assessed using more sensitive techniques such as the Agilent 2100 Bioanalyzer 6000 RNA Nano Chip.
  • the locus link ID can be used to determine the sequence of all the RNA products and all the protein products of the biomarkers of the invention.
  • combinations of biomarkers of the present invention includes any combination of the biomarkers listed in Table 1 , Table 2 , Table 11 , or Table 12 .
  • Table 1 the number of possible combinations of a subset n of m genes in any of the tables above is described in Feller, Intro to Probability Theory, Third Edition, volume 1, 1968, ed. J. Wiley , using the general formula: m ! / n ! m - n !
  • biomarkers which demonstrate a p value of greater than 0.2 do significantly increase the ability of a combination of biomarkers in which they are included to distinguish as between two phenotypic trait subgroups.
  • biomarkers for input into the model to test in combination are chosen on the basis of the fold change of differential expression of the product of the biomarker as between the the two phenotypic trait subgroups.
  • selection of biomarker subsets for input into classifier is based on a differential fold change where the fold change is greater than 1.01, 1.02, 1.03, 1.04, 1.05, 1.06, 1.07, 1.08, 1.09, 1.1, 1.125, 1.15, 1.175, 1, 1.2, 1.225, 1.25, 1.275, 1.30, greater than 1.3, greater than 1.4, greater than 1.5, greater than 1.6, greater than 1.7, greater than 1.8, greater than 1.9, greater than 2.0, greater than 2.1, greater than 2.2, greater than 2.3, greater than 2.4, greater than 2.5, greater than 2.6, greater than 2.7, greater than 2.8, greater than 2.9, greater than 3.0, greater than 3.1, greater than 3.2.
  • the desired number of selected biomarkers can be 4,000; 3,000; 2,000; 1,000; 900; 800; 700; 600; 500; 400; 300; 200; 190; 180; 170; 160; 150; 140; 130; 120; 110; 100; 90; 80; 70; 60; 50; 40; 30; 20; or 10.
  • the selection criteria noted above can be set on the basis of the desired number of selected biomarkers for use in the model. As would be understood, one can select therefore all of the individually identified biomarkers or subsets of the individually identified biomarkers and test all possible combinations of the selected biomarkers to identify useful combinations of biomarkers.
  • a selection criteria to determine the number of selected individual biomarkers to test in combination, and to select the number of possible combinations of biomarkers will depend upon the resources available for obtaining the biomarker data and/or the computer resources available for calculating and evaluating classifiers resulting from the model.
  • the classifier generated by the mathematical model can be subsequently evaluated by determining the ability of the classifier to correctly call each individual for one of the two phenotypic traits of the population used to generate the classifier (ie having or not having one or more colorectal pathologies).
  • the individuals of the training population used to derive the model are different from the individuals of the training population used to test the model. As would be understood by a person skilled in the art, this allows one to predict the ability of the combinations as to their ability to properly characterize an individual whose phenotypic trait characterization is unknown.
  • the data which is input into the mathematical model can be any data which is representative of the expression level of the product of the biomarkers being evaluated.
  • Mathematical models useful in accordance with the invention include those using both supervised or unsupervised learning techniques.
  • the mathematical model chosen uses supervised learning in conjunction with a "training population" to evaluate each of the possible combination of biomarkers of the invention.
  • a formula is generated which utilizes more than one classifier.
  • a formula can be generated which utilizes classifiers in series (e.g. first obtains results of classifier A, then classifier B e.g. Classifier A differentiates pathology from non pathology; classifier B then determines whether the pathology is colorectal cancer or not colorectal cancer).
  • a formula can be generated which results from weighting the results of more than one classifier.
  • each classifier can be given a score of 1 and an indication of probability of a test subject having one or more colorectal pathologies is the result of the aggregate score of each of the selected classifiers of a given formula.
  • Other possible combinations and weightings of classifiers would be understood and are encompassed herein.
  • Classifiers generated can be used to test an unknown or test subject.
  • the results from equations generated by logistic regression to answer the question does an individual have one or more colorectal pathologies or is an individual "normal".
  • the answer to the question above may be an answer of non-determinable.
  • the method used to evaluate the classifier for its ability to properly characterize each individual of the training population is a method which evaluates the classifier's sensitivity (TPF, true positive fraction) and 1-specificity (TNF, true negative fraction).
  • the method used to test the classifier is Receiver Operating Characteristic ("ROC") which provides several parameters to evaluate both the sensitivity and specificity of the result of the equation generated.
  • ROC Receiver Operating Characteristic
  • the ROC area area under the curve
  • a perfect ROC area score of 1.0 indicates with both 100% sensitivity and 100% specificity.
  • classifiers are selected on the basis of the score.
  • ROC receiver operating characteristic
  • those classifiers with scores of greater than 0.95, 0.9, 0.85, 0.8, 0.7, 0.65, 0.6, 0.55 0.5 or 0.45 are chosen.
  • a sensitivity threshold can be set and classifiers ranked on the basis of the specificity chosen. For example classifiers with a cutoff for specificity of greater than 0.95, 0.9, 0.85, 0.8, 0.7, 0.65, 0.6, 0.55 0.5 or 0.45 can be chosen.
  • the specificity threshold can be set and classifiers ranked on the basis of sensitivity greater than 0.95, 0.9, 0.85, 0.8, 0.7, 0.65, 0.6, 0.55 0.5 or 0.45 can be chosen.
  • sensitivity greater than 0.95, 0.9, 0.85, 0.8, 0.7, 0.65, 0.6, 0.55 0.5 or 0.45 can be chosen.
  • only the top 10 ranking classifiers, the top 20 ranking classifiers, or the top 100 ranking classifiers are selected.
  • the reference or training population includes between 10 and 30 subjects. In another embodiment the reference population contains between 30-50 subjects. In still other embodiments, the reference population includes two or more populations each containing between 50 and 100, 100 and 500, between 500 and 1000, or more than 1000 subjects.
  • the reference population includes two or more subpopulations. In a preferred embodiment, the phenotypic trait characteristics of the subpopulations are similar but for the diagnosis with respect to the presence of one or more colorectal pathologies, for example the distribution within the subpopulations are similar with regards to the age and sex of the subpopulations. It is also preferred that the subpopulations are of roughly equivalent numbers. It is to be understood that the methods herein do not require using data from every member of a population, but instead may rely on data from a subset of a population in question.
  • the reference population is comprised of individuals having polyps (the first subpopulation), and individuals not having polyps (the second subpopulation).
  • any verified method can be used including digital rectal examiniation, fecal occult blood testing, rigid sigmoidoscopy, flexible sigmoidoscopy, double-contrast barium enema, colonoscopy, and histological examination.
  • Preferably only those individuals whose diagnoses are certain are utilized as part of the reference population.
  • the reference population is comprised of individuals having high risk polyps (the first subpopulation), and individuals not having high risk polyps (the second subpopulation) where high risk polyps are the following: Tubulovillous Adenoma, Villous Adenoma, Cancer High Grade Dysplasia and Tubular Adenoma where the Tubular Adenoma is greater than 10mm.
  • any verified method can be used including digital rectal examiniation, fecal occult blood testing, rigid sigmoidoscopy, flexible sigmoidoscopy, double-contrast barium enema, colonoscopy, and histological examination.
  • the reference population can, for example be comprised of individuals having localized colorectal cancer as compared with individuals with other types of colorectal cancer (e.g. late stage).
  • the reference population is comprised of individuals having high risk polyps (the first subpopulation), and individuals not having high risk polyps (the second subpopulation) where high risk polyps are the following: Tubulovillous Adenoma; Villous Adenoma; Cancer; High Grade Dysplasia; and Tubular Adenoma.
  • the RNA products of the biomarkers of the invention which are measured are the population of RNA products including the mRNA, and all of the spliced variants of the mRNA.
  • the products measured are all of the mRNA products expressed in blood.
  • the products measured include one or more specific spliced variants of the mRNA which are expressed in blood.
  • the products measured are the RNA products listed in Table 3 or Table 13 .
  • Protein products of the biomarkers of the invention are also included within the scope of the invention.
  • measurement of the protein products of the biomarkers of the invention can be used for purposes of testing for one or more colorectal pathologies. More particularly, measurement of those populations of protein products of the biomarkers which are differentially expressed in individuals having or not having any polyps are useful for purposes of testing and are encompassed herein.
  • the protein products are those translated from the biomarkers listed in Table 1, Table 2, Table 11, or Table 12 .
  • the protein products are those which are expressed in blood.
  • the protein products are those corresponding to the proteins listed in Table 3 or Table 13.
  • V might be an actual probability (a number varying between 0 and 1), or V might be a quantity from which a probability can be readily derived.
  • the expression data for some or all of the biomarkers identified in the present invention are used in a regression model, such as but not limited to a logistic regression model or a linear regression model, so as to identify classifiers useful in diagnosing one or more colorectal pathologies.
  • the regression model is used to test various combinations of two or more of the biomarkers identified in Table 1 , Table 2 , Table 11 , or Table 12 to generate classifiers.
  • the classifiers which result are in the form of equations which provide a dependent variable Y, which represents the presence or absence of a given phenotype where the data representing the expression of each of the biomarkers in the equation is multiplied by a weighted coefficient as generated by the regression model.
  • the dependent variable Y depends on k explanatory variables (the measured characteristic values for the k select genes (e.g., the biomarkers) from subjects in the first and second subgroups in the reference population), plus an error term that encompasses various unspecified omitted factors.
  • the parameter ⁇ 1 gauges the effect of the first explanatory variable Xi on the dependent variable Y (e.g., a weighting factor), holding the other explanatory variables constant.
  • ⁇ 2 gives the effect of the explanatory variable X 2 on Y, holding the remaining explanatory variables constant.
  • the logistic regression model is fit by maximum likelihood estimation (MLE).
  • MLE maximum likelihood estimation
  • the coefficients e.g., ⁇ , ⁇ 1 , ⁇ 2 , ...) are determined by maximum likelihood.
  • a likelihood is a conditional probability (e.g., P(Y/X), the probability of Y given X).
  • MLE involves finding the coefficients ⁇ , ⁇ 1 , ⁇ 2 , ...) that makes the log of the likelihood function (LL ⁇ 0) as large as possible or -2 times the log of the likelihood function (-2LL) as small as possible.
  • some initial estimates of the parameters ⁇ , ⁇ 1 , ⁇ 2 , ... are made.
  • the likelihood of the data given these parameter estimates is computed.
  • the parameter estimates are improved the likelihood of the data is recalculated. This process is repeated until the parameter estimates do not change much (for example, a change of less than .01 or .001 in the probability). Examples of logistic regression and fitting logistic logistic regression models are found in Hastie, The Elements of Statistical Learning, Springer, New York, 2001, pp. 95-100 which is incorporated herein in its entirety.
  • the expression measured for each of the biomarkers of the present invention can be used to train a neural network.
  • a neural network is a two-stage regression or classification model.
  • a neural network can be binary or non binary.
  • a neural network has a layered structure that includes a layer of input units (and the bias) connected by a layer of weights to a layer of output units. For regression, the layer of output units typically includes just one output unit.
  • neural networks can handle multiple quantitative responses in a seamless fashion. As such a neural network can be applied to allow identification of biomarkers which differentiate as between more than two populations (ie more than two phenotypic traits).
  • a neural network can be trained using expression data from the products of the biomarkers in Table 1, Table 2, Table 11, or Table 12 to identify those combinations of biomarkers which are specific for one or more colorectal pathologies.
  • the trained neural network can be used to directly identify combinations of biomarkers useful to test for one or more colorectal pathologies.
  • the back-propagation neural network (see, for example Abdi, 1994, "A neural network primer", J. Biol System. 2, 247-283 ) containing a single hidden layer of ten neurons (ten hidden units) found in EasyNN-Plus version 4.0g software package (Neural Planner Software Inc.) is used.
  • Neural networks are described in Duda et al., 2001, Pattern Classification, Second Edition, John Wiley & Sons, Inc., New York ; and Hastie et al., 2001, The Elements of Statistical Learning, Springer-Verlag, New York which is incorporated herein in its entirety.
  • the ordering of the singular vectors is determined by high-to-low sorting of singular values, with the highest singular value in the upper left index of the S matrix. Note that for a square, symmetric matrix X, singular value decomposition is equivalent to diagonalization, or solution of the eigenvalue problem.
  • the pattern classification and statistical techniques described above are merely examples of the types of models that can be used to construct classifiers useful for diagnosing or detecting one or more colorectal pathologies, for example clustering as described on pages 211-256 of Duda and Hart, Pattern Classification and Scene Analysis, 1973, John Wiley & Sons, Inc., New York , incorporated herein by reference in its entirety; Principal component analysis, (see for Jolliffe, 1986, Principal Component Analysis, Springer, New York , incorporated herein by reference); nearest neighbour classifier analysis, (see for example Duda, Pattern Classification, Second Edition, 2001, John Wiley & Sons, Inc ; and Hastie, 2001, The Elements of Statistical Learning, Springer, New York ); linear discriminant analysis, (see for example Duda, Pattern Classification, Second Edition, 2001, John Wiley & Sons, Inc ; and Hastie, 2001, The Elements of Statistical Learning, Springer, New York ; Venables & Ripley, 1997, Modern Applied Statistics with
  • the computer system may have access or be accessible to "the internet" [World Wide Web (WWW)]. It will be appreciated that the computer system may be a stand-alone system or a distributed system comprising multiple devices communicating with each other through a network. Depending on the application and purpose, the computer system may be a static or mobile computer system.
  • WWW World Wide Web
  • Suitable programming languages for expressing the program instructions include, but are not limited to, one or more languages selected from the group consisting of: C, C++, an embodiment of FORTRAN such as FORTRAN77 or FORTRAN90, Java, Visual Basic, Perl, Tcl/Tk, JavaScript, and ADA. It is to be understood that various aspects of the methods may be written in different computing languages from one another, where such languages are preferred for particular applications, and the various aspects are caused to communicate with one another by appropriate system-level-tools available on a given computer.
  • the computer program instructions are stored in a computer memory during execution, and may additionally be stored on any of various forms of computer-readable media known in the art, such as, but not limited to, CD-Rom, CD-R, CD-RW, flash memory, memory cards, memory sticks, DVD-Rom, USB-sticks, optical discs, or high capacity network storage drives. It is thus consistent with ordinary practice of the present invention that the computer program instructions can be delivered to a user on a transferable medium such as a CD-Rom, and also delivered over a computer network, such as by downloading over the Internet through a web-interface.
  • a transferable medium such as a CD-Rom
  • FIG. 1 shows a schematic of a general-purpose computer system 100 suitable for practicing the methods described herein.
  • the computer system 100 shown as a self-contained unit but not necessarily so limited, comprises at least one data processing unit (CPU) 102, a memory 104, which will typically include both high speed random access memory as well as non-volatile memory (such as one or more magnetic disk drives) but may be simply flash memory, a user interface 108, optionally a disk 110 controlled by a disk controller 112, and at least one optional network or other communication interface card 114 for communicating with other computers as well as other devices.
  • At least the CPU 102, memory 104, user interface 108, disk controller where present, and network interface card communicate with one another via at least one communication bus 106.
  • Memory 104 stores procedures and data, typically including: an operating system 140 for providing basic system services; application programs 152 such as user level programs for viewing and manipulating data, evaluating formulae for the purpose of diagnosing a test subject; authoring tools for assisting with the writing of computer programs; a file system 142, a user interface controller 144 for handling communications with a user via user interface 108, and optionally one or more databases 146 for storing microarray data and other information, optionally a graphics controller 148 for controlling display of data, and optionally a floating point coprocessor 150 dedicated to carrying out mathematical operations.
  • the methods of the present invention may also draw upon functions contained in one or more dynamically linked libraries, not shown in FIG. 1 , but stored either in Memory 104, or on disk 110, or accessible via network interface connection 114.
  • User interface 108 may comprise a display 128, a mouse 126, and a keyboard 130. Although shown as separate components in FIG. 1 , one or more of these user interface components can be integrated with one another in embodiments such as handheld computers.
  • Display 128 may be a cathode ray tube (CRT), or flat-screen display such as an LCD based on active matrix or TFT embodiments, or may be an electroluminescent display, based on light emitting organic molecules such as conjugated small molecules or polymers.
  • CTR cathode ray tube
  • LCD liquid crystal display
  • a security-device such as a fingerprint sensor or a retinal scanner that prohibits an unauthorized user from accessing data and programs stored in system 100.
  • System 100 may also be connected to an output device such as a printer (not shown), either directly through a dedicated printer cable connected to a serial or USB port, or wirelessly, or via a network connection.
  • an output device such as a printer (not shown)
  • printer either directly through a dedicated printer cable connected to a serial or USB port, or wirelessly, or via a network connection.
  • the database 146 may instead, optionally, be stored on disk 110 in circumstances where the amount of data in the database is too great to be efficiently stored in memory 104.
  • the database may also instead, or in part, be stored on one or more remote computers that communicate with computer system 100 through network interface connection 114.
  • a user may use a handheld embodiment that accepts data from a test subject, and transmits that data across a network connection to another device or location wherein the data is analyzed according to a formulae described herein.
  • a result of such an analysis can be stored at the other location and/or additionally transmitted back to the handheld embodiment.
  • the act of accepting data from a test subject can include the act of a user inputting the information.
  • the network connection can include a web-based interface to a remote site at, for example, a healthcare provider.
  • system 10 can be a device such as a handheld device that accepts data from the test subject, analyzes the data, such as by inputting the data into a formula as further described herein, and generating a result that is displayed to the user. The result can then be, optionally, transmitted back to a remote location via a network interface such as a wireless interface.
  • System 100 may further be configured to permit a user to transmit by e-mail results of an analysis directly to some other party, such as a healthcare provider, or a diagnostic facility, or a patient.
  • the identification of one or more biomarkers can be used to allow for the testing, screening or diagnosis of one or more colorectal pathologies including polyps or one or more subtypes of polyps within a test subject by measuring the expression of the products of the biomarkers (gene) in the test subject (the "test subject").
  • Data representative of the products of the biomarkers of the invention (including RNA and/or Protein) is input into a formula of the invention so as to determine a probability of a test subject having one or more colorectal pathologies.
  • the data can be generated using any technique known to measure the level of expression of either the RNA and protein products of the biomarkers of the invention.
  • use of the formula results in a determination of whether the test subject has polyps or does not have polyps.
  • Y is used as a predictor of polyps, where when Y > 0 a person is diagnosed as having polyps and where Y ⁇ 0, a person is diagnosed as not having polyps.
  • Polynucleotides capable of specifically or selectively binding to the RNA products of the biomarkers of the invention are used to measure the level of expression of the biomarkers.
  • oligonucleotides, cDNA, DNA, RNA, PCR products, synthetic DNA, synthetic RNA, or other combinations of naturally occurring or modified nucleotides which specifically and/or selectively hybridize to one or more of the RNA products of the biomarker of the invention are useful in accordance with the invention.
  • the oligonucleotides, cDNA, DNA, RNA, PCR products, synthetic DNA, synthetic RNA, or other combinations of naturally occurring or modified nucleotides oligonucleotides which both specifically and selectively hybridize to one or more of the RNA products of the biomarker of the invention are used.
  • the polynucleotide used to measure the RNA products of the biomarkers of the invention can be used as nucleic acid members localized on a support to comprise an array according to one aspect of the invention.
  • the length of a nucleic acid member can range from 8 to 1000 nucleotides in length and are chosen so as to be specific for the RNA products of the biomarkers of the invention. In one embodiment, these members are selective for the RNA products of the biomarkers of the invention.
  • the nucleic acid members may be single or double stranded, and/or may be oligonucleotides or PCR fragments amplified from cDNA. In some embodiments oligonucleotides are approximately 20-30 nucleotides in length.
  • ESTs are in some embodiments 100 to 600 nucleotides in length. It will be understood to a person skilled in the art that one can utilize portions of the expressed regions of the biomarkers of the invention as a probe on the array. More particularly oligonucleotides complementary to the genes of the invention and or cDNA or ESTs derived from the genes of the invention are useful. For oligonucleotide based arrays, the selection of oligonucleotides corresponding to the gene of interest which are useful as probes is well understood in the art. More particularly it is important to choose regions which will permit hybridization to the target nucleic acids. Factors such as the Tm of the oligonucleotide, the percent GC content, the degree of secondary structure and the length of nucleic acid are important factors. See for example US Patent No. 6,551,784 .
  • microarrays can be used to identify and select genes differentially expressed in individuals having or not having one or more colorectal pathologies, one or more polyps or one or more subtypes of polyps, and can be used to diagnose or detect polyps or one or more subtypes of polyps using the biomarkers of the invention.
  • Genes identified as differentially expressed using microarrays can be seen in Table 1, and Table 11.
  • the nucleic acid members may be produced using established techniques such as polymerase chain reaction (PCR) and reverse transcription (RT). These methods are similar to those currently known in the art (see e.g., PCR Strategies, Michael A. Innis (Editor), et al. (1995 ) and PCR: Introduction to Biotechniques Series, C. R. Newton, A. Graham (1997 )).
  • Amplified nucleic acids are purified by methods well known in the art (e.g., column purification or alcohol precipitation).
  • a nucleic acid is considered pure when it has been isolated so as to be substantially free of primers and incomplete products produced during the synthesis of the desired nucleic acid.
  • a purified nucleic acid will also be substantially free of contaminants which may hinder or otherwise mask the specific binding activity of the molecule.
  • An array comprises a plurality of nucleic acids attached to one surface of a support at a density exceeding 20 different nucleic acids/cm 2 , wherein each of the nucleic acids is attached to the surface of the support in a non-identical pre-selected region (e.g. a microarray).
  • Each associated sample on the array comprises a nucleic acid composition, of known identity, usually of known sequence, as described in greater detail below. Any conceivable substrate may be employed in the invention.
  • the nucleic acid attached to the surface of the support is DNA. In a preferred embodiment, the nucleic acid attached to the surface of the support is cDNA or RNA. In another preferred embodiment, the nucleic acid attached to the surface of the support is cDNA synthesized by polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • a nucleic acid member in the array, according to the invention is at least 10, 25 or 50 nucleotides in length. In one embodiment, a nucleic acid member is at least 150 nucleotides in length. In some embodiments, a nucleic acid member is less than 1000 nucleotides in length. More preferably, a nucleic acid member is less than 500 nucleotides in length.
  • the nucleic acid compositions are stably associated with the surface of a support.
  • the support may be a flexible or rigid support.
  • stably associated is meant that each nucleic acid member maintains a unique position relative to the support under hybridization and washing conditions.
  • the samples are non-covalently or covalently stably associated with the support surface. Examples of non-covalent association include non-specific adsorption, binding based on electrostatic interactions (e.g., ion pair interactions), hydrophobic interactions, hydrogen bonding interactions, specific binding through a specific binding pair member covalently attached to the support surface, and the like.
  • covalent binding examples include covalent bonds formed between the nucleic acids and a functional group present on the surface of the rigid support (e.g., --OH), where the functional group may be naturally occurring or present as a member of an introduced linking group, as described in greater detail below
  • each composition will be sufficient to provide for adequate hybridization and detection of target nucleic acid sequences during the assay in which the array is employed.
  • the amount of each nucleic acid member stably associated with the support of the array is at least about 0.001 ng, preferably at least about 0.02 ng and more preferably at least about 0.05 ng, where the amount may be as high as 1000 ng or higher, but will usually not exceed about 20 ng.
  • the diameter of the "spot” will generally range from about 10 to 5,000 ⁇ m, usually from about 20 to 2,000 ⁇ m and more usually from about 100 to 200 ⁇ m.
  • Control nucleic acid members may be present on the array including nucleic acid members comprising oligonucleotides or nucleic acids corresponding to genomic DNA, housekeeping genes, vector sequences, plant nucleic acid sequence, negative and positive control genes, and the like. Control nucleic acid members are calibrating or control genes whose function is not to tell whether a particular "key" gene of interest is expressed, but rather to provide other useful information, such as background or basal level of expression.
  • control nucleic acids are spotted on the array and used as target expression control nucleic acids and mismatch control nucleotides to monitor non-specific binding or cross-hybridization to a nucleic acid in the sample other than the target to which the probe is directed.
  • Mismatch probes thus indicate whether a hybridization is specific or not. For example, if the target is present, the perfectly matched probes should be consistently brighter than the mismatched probes. In addition, if all control mismatches are present, the mismatch probes are used to detect a mutation.
  • Nucleic acid arrays according to the invention can be used to assay nucleic acids in a sample comprising one or more target nucleic acid sequences (ie such as RNA products of the biomarkers of the invention).
  • the arrays of the subject invention can be used for testing, screening, and/or diagnosis of one or more colorectal pathologies including polyps or one or more subtypes of polyps, or screening for therapeutic targets and the like.
  • the arrays are also useful in broad scale expression screening for drug discovery and research, such as the effect of a particular active agent on the expression pattern of biomarkers of the invention, where such information is used to reveal drug efficacy and toxicity, environmental monitoring, disease research and the like.
  • Arrays can be made using at least one, more preferably a combination of these sequences, as a means of diagnosing colon pathology or one or more subtypes of colon pathology.
  • RNA isolated from one or more normal individuals wherein a normal individual is an individual not having polyps.
  • the samples for hybridization with the arrays according to the invention are in some embodiments derived from total RNA from blood.
  • targets for the arrays are derived from mRNA from blood.
  • the nucleic acid sample is capable of binding to a nucleic acid member of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation.
  • nucleic acid derived from an mRNA transcript or a “nucleic acid corresponding to an mRNA” refers to a nucleic acid for which synthesis of the mRNA transcript or a sub-sequence thereof has ultimately served as a template.
  • a cDNA reverse transcribed from an mRNA, an RNA transcribed from that cDNA, a DNA amplified from the cDNA, an RNA transcribed from the amplified DNA, etc. are all derived from or correspond to the mRNA transcript and detection of such derived or corresponding products is indicative of or proportional to the presence and/or abundance of the original transcript in a sample.
  • suitable nucleic acid samples include, but are not limited to, mRNA transcripts of a gene or genes, cDNA reverse transcribed from the mRNA, cRNA transcribed from the cDNA, DNA amplified from a gene or genes, RNA transcribed from amplified DNA, and the like.
  • the nucleic acid samples used herein are in some embodiments derived from blood.
  • Nucleic acids can be single- or double-stranded DNA, RNA, or DNA-RNA hybrids synthesized from human blood using methods known in the art, for example, reverse transcription or PCR.
  • such a nucleic acid sample comprises total mRNA or a nucleic acid sample corresponding to mRNA (e.g., cDNA) isolated from blood samples.
  • total mRNA is isolated from a given sample using, for example, an acid guanidinium-phenol-chloroform extraction method and polyA+ mRNA is isolated by oligo dT column chromatography or by using (dT)n magnetic beads (see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed.), Vols. 1-3, Cold Spring Harbor Laboratory, (1989 ), or Current Protocols in Molecular Biology, F. Ausubel et al., ed.
  • RNA is extracted using TRIzo1® reagent (GIBCO/BRL, Invitrogen Life Technologies, Cat. No. 15596). Purity and integrity of RNA is assessed by absorbance at 260/280nm and agarose gel electrophoresis followed by inspection under ultraviolet light.
  • sample e.g. drop of blood
  • amplification method if a quantitative result is desired, care must be taken to use a method that maintains or controls for the relative frequencies of the amplified nucleic acids.
  • Methods of "quantitative" amplification are well known to those of skill in the art. For example, quantitative PCR involves simultaneously co-amplifying a known quantity of a control sequence using the same primers. This provides an internal standard that may be used to calibrate the PCR reaction.
  • the high density array may then include probes specific to the internal standard for quantification of the amplified nucleic acid.
  • Detailed protocols for quantitative PCR are provided in PCR Protocols, A Guide to Methods and Applications, Innis et al., Academic Press,'Inc. N.Y., (1990 ).
  • PCR polymerase chain reaction
  • LCR ligase chain reaction
  • the nucleic acid sample mRNA is reverse transcribed with a reverse transcriptase and a primer consisting of oligo dT and a sequence encoding the phage T7 promoter to provide single-stranded DNA template.
  • the second DNA strand is polymerized using a DNA polymerase.
  • T7 RNA polymerase is added and RNA is transcribed from the cDNA template. Successive rounds of transcription from each single cDNA template results in amplified RNA.
  • Nucleic acid samples are labelled so as to allow detection of hybridization to an array of the invention.
  • Any analytically detectable marker that is attached to or incorporated into a molecule may be used in the invention.
  • An analytically detectable marker refers to any molecule, moiety or atom which is analytically detected and quantified.
  • Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
  • Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., DynabeadsTM), fluorescent dyes (e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., 3 H, 125 I,35S, 14 C, or 32 P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.
  • fluorescent dyes e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and
  • Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837 ; 3,850,752 ; 3,939,350 ; 3,996,345 ; 4,277,437 ; 4,275,149 ; and 4,366,241 , the entireties of which are incorporated by reference herein.
  • radiolabels may be detected using photographic film or scintillation counters
  • fluorescent markers may be detected using a photodetector to detect emitted light
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
  • the labels may be incorporated by any of a number of means well known to those of skill in the art. However, in one embodiment, the label is simultaneously incorporated during the amplification step in the preparation of the sample nucleic acids.
  • PCR polymerase chain reaction
  • labeled primers or labeled nucleotides will provide a labeled amplification product.
  • transcription amplification as described above, using a labeled nucleotide (e.g. fluorescein-labeled UTP and/or CTP) incorporates a label into the transcribed nucleic acids.
  • a label may be added directly to the original nucleic acid sample (e.g., mRNA, polyA mRNA, cDNA, etc.) or to the amplification product after the amplification is completed.
  • Means of attaching labels to nucleic acids are well known to those of skill in the art and include, for example, nick translation or end-labeling (e.g. with a labeled RNA) by kinasing of the nucleic acid and subsequent attachment (ligation) of a nucleic acid linker joining the sample nucleic acid to a label (e.g., a fluorophore).
  • the fluorescent modifications are by cyanine dyes e.g. Cy-3/Cy-5 dUTP, Cy-3/Cy-5 dCTP (Amersham Pharmacia) or alexa dyes ( Khan,et al., 1998, Cancer Res. 58:5009-5013 ).
  • cyanine dyes e.g. Cy-3/Cy-5 dUTP, Cy-3/Cy-5 dCTP (Amersham Pharmacia) or alexa dyes ( Khan,et al., 1998, Cancer Res. 58:5009-5013 ).
  • the two Nucleic Acid Sample samples used for comparison are labeled with different fluorescent dyes which produce distinguishable detection signals, for example, nucleic acid samples made from normal intestinal cells are labeled with Cy5 and nucleic acid samples made from intestinal tissue cells are labeled with Cy3.
  • the differently labeled target samples are hybridized to the same microarray simultaneously.
  • the labeled nucleic acid samples are purified using methods known in the art, e.g., by ethanol purification or column purification.
  • the nucleic acid samples will include one or more control molecules which hybridize to control probes on the microarray to normalize signals generated from the microarray.
  • labeled normalization nucleic acid samples are nucleic acid sequences that are perfectly complementary to control oligonucleotides that are spotted onto the microarray as described above.
  • labeled normalization nucleic acid samples are nucleic acid sequences that are 99%, 98%, 97%, 96%, 95%, 90%, 85%, 80% or 75% complementary to control oligonucleotides that are spotted onto the microarray as described above.
  • the signals obtained from the normalization controls after hybridization provide a control for variations in hybridization conditions, label intensity, "reading" efficiency and other factors that may cause the signal of a perfect hybridization to vary between arrays.
  • signals (e.g., fluorescence intensity) read from all other probes in the array are divided by the signal (e.g., fluorescence intensity) from the control probes, thereby normalizing the measurements.
  • Preferred normalization nucleic acid samples are selected to reflect the average length of the other nucleic acid samples present in the sample, however, they are selected to cover a range of lengths.
  • the normalization control(s) also can be selected to reflect the (average) base composition of the other probes in the array, however, in one embodiment, only one or a few normalization probes are used and they are selected such that they hybridize well (i.e., have no secondary structure and do not self hybridize) and do not match any nucleic acids on the array.
  • Normalization probes are localized at any position in the array or at multiple positions throughout the array to control for spatial variation in hybridization efficiency.
  • normalization controls are located at the corners or edges of the array as well as in the middle.
  • Nucleic acid hybridization involves providing a nucleic acid sample under conditions where the sample and the complementary nucleic acid member can form stable hybrid duplexes through complementary base pairing. The nucleic acids that do not form hybrid duplexes are then washed away leaving the hybridized nucleic acids to be detected, typically through detection of an attached detectable label. It is generally recognized that nucleic acids are denatured by increasing the temperature or decreasing the salt concentration of the buffer containing the nucleic acids. Under low stringency conditions (e.g., low temperature and/or high salt) hybrid duplexes (e.g., DNA:DNA, RNA:RNA, or RNA:DNA) will form even where the annealed sequences are not perfectly complementary. Thus specificity of hybridization is reduced at lower stringency. Conversely, at higher stringency (e.g., higher temperature or lower salt) successful hybridization requires fewer mismatches.
  • low stringency conditions e.g., low temperature and/or high salt
  • the invention provides for hybridization conditions comprising the Dig hybridization mix (Boehringer); or formamide-based hybridization solutions, for example as described in Ausubel et al., supra and Sambrook et al. supra.
  • the resultant hybridization pattern is detected.
  • the intensity or signal value of the label will be not only be detected but quantified, by which is meant that the signal from each spot of the hybridization will be measured and compared to a unit value corresponding to the signal emitted by a known number of end labeled target nucleic acids to obtain a count or absolute value of the copy number of each end-labeled target that is hybridized to a particular spot on the array in the hybridization pattern.
  • data analysis can include the steps of determining fluorescent intensity as a function of substrate position from the data collected, removing outliers, i.e., data deviating from a predetermined statistical distribution, and calculating the relative binding affinity of the test nucleic acids from the remaining data.
  • the resulting data is displayed as an image with the intensity in each region varying according to the binding affinity between associated oligonucleotides and/or nucleic acids and the test nucleic acids.
  • the following detection protocol is used for the simultaneous analysis of two samples to be compared, where each sample is labeled with a different fluorescent dye.
  • Each element of the microarray is scanned for the first fluorescent color.
  • the intensity of the fluorescence at each array element is proportional to the expression level of that gene in the sample.
  • the scanning operation is repeated for the second fluorescent label.
  • the ratio of the two fluorescent intensities provides a highly accurate and quantitative measurement of the relative gene expression level in the two samples.
  • fluorescence intensities of immobilized nucleic acid sequences were determined from images taken with a custom confocal microscope equipped with laser excitation sources and interference filters appropriate for the Cy3 and Cy5 fluors. Separate scans were taken for each fluor at a resolution of 225 ⁇ m 2 per pixel and 65,536 gray levels. Image segmentation to identify areas of hybridization, normalization of the intensities between the two fluor images, and calculation of the normalized mean fluorescent values at each target are as described ( Khan, et al., 1998, Cancer Res. 58:5009-5013 . Chen, et al., 1997, Biomed. Optics 2:364-374 ). Normalization between the images is used to adjust for the different efficiencies in labeling and detection with the two different fluors. This is achieved by equilibrating to a value of one the signal intensity ratio of a set of internal control genes spotted on the array.
  • the array is scanned in the Cy3 and Cy5 channels and stored as separate 16-bit TIFF images.
  • the images are incorporated and analysed using software which includes a gridding process to capture the hybridization intensity data from each spot on the array.
  • the fluorescence intensity and background-subtracted hybridization intensity of each spot is collected and a ratio of measured mean intensities of Cy5 to Cy3 is calculated.
  • a linear regression approach is used for normalization and assumes that a scatter plot of the measured Cy5 versus Cy3 intensities should have a slope of one.
  • the average of the ratios is calculated and used to rescale the data and adjust the slope to one.
  • a ratio of expression not equal to 1 is used as an indication of differential gene expression.
  • the nucleic acid sample is one in which the concentration of the mRNA transcript(s) of the gene or genes, or the concentration of the nucleic acids derived from the mRNA transcript(s), is proportional to the transcription level (and therefore expression level) of that gene.
  • the hybridization signal intensity be proportional to the amount of hybridized nucleic acid.
  • the proportionality be relatively strict (e.g., a doubling in transcription rate results in a doubling in mRNA transcript in the sample nucleic acid pool and a doubling in hybridization signal), one of skill will appreciate that the proportionality can be more relaxed and even non-linear and still provide meaningful results.
  • an assay where a 5 fold difference in concentration of the sample mRNA results in a 3- to 6-fold difference in hybridization intensity is sufficient for most purposes.
  • appropriate controls are run to correct for variations introduced in sample preparation and hybridization as described herein.
  • serial dilutions of "standard" mRNA samples are used to prepare calibration curves according to methods well known to those of skill in the art. Of course, where simple detection of the presence or absence of a transcript is desired, no elaborate control or calibration is required.
  • nucleic acid member on an array is not labeled after hybridization, this indicates that the gene comprising that nucleic acid member is not expressed in either sample. If a nucleic acid member is labeled with a single color, it indicates that a labeled gene was expressed only in one sample. The labeling of a nucleic acid member comprising an array with both colors indicates that the gene was expressed in both samples. Even genes expressed once per cell are detected (1 part in 100,000 sensitivity).
  • a typical reaction mixture includes: 2 ml of DNA, 25 pmol of oligonucleotide primer, 2.5 ml of 10H PCR buffer 1 (Perkin-Elmer, Foster City, CA), 0.4 ml of 1.25 mM dNTP, 0.15 ml (or 2.5 units) of Taq DNA polymerase (Perkin Elmer, Foster City, CA) and deionized water to a total volume of 25 ml. Mineral oil is overlaid and the PCR is performed using a programmable thermal cycler.
  • Detection can also be accomplished using any of a variety of other immunoassays.
  • a radioimmunoassay RIA
  • the radioactive isotope e.g., 125 I, 131 I, 35 S or s H
  • a gamma counter or a scintillation counter can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography.
  • Polypeptides for the array can be spotted at high speed, e.g., using commercially available robotic apparatus, e.g., from Genetic MicroSystems and Affymetrix (Santa Clara, California, USA) or BioRobotics (Cambridge, UK).
  • the array substrate can be, for example, nitrocellulose, plastic, glass, e.g., surface-modified glass.
  • the array can also include a porous matrix, e.g., acrylamide, agarose, or another polymer.
  • the array can be an array of antibodies, e.g., as described in De Wildt, supra.
  • Cells that produce the polypeptide ligands can be grown on a filter in an arrayed format. Polypeptide production is induced, and the expressed antibodies are immobilized to the filter at the location of the cell. Information about the extent of binding at each address of the array can be stored as a profile, e.g., in a computer database.
  • Standard recombinant nucleic acid methods can be used to express a polypeptide or antibody of the invention (e.g., a protein products of a biomarker of the invention).
  • a nucleic acid sequence encoding the polypeptide is cloned into a nucleic acid expression vector.
  • each chain must be cloned into an expression vector, e.g., the same or different vectors, that are expressed in the same or different cells.
  • the protein is sufficiently small, i.e., the protein is a peptide of less than 50 amino acids, the protein can be synthesized using automated organic synthetic methods.
  • Bacterial pBs, phagescript, PsiX174, pBluescript SK, pBs KS, pNH8a, pNH16a, pNH18a, pNH46a (Stratagene, La Jolla, California, USA); pTrc99A, pKK223-3, pKK233-3, pDR540, and pRIT5 (Pharmacia, Uppsala, Sweden).
  • Eukaryotic pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVK3, pBPV, pMSG, and pSVL (Pharmacia).
  • One preferred class of preferred libraries is the display library, which is described below.
  • Methods well known to those skilled in the art can be used to construct vectors containing a polynucleotide of the invention and appropriate transcriptional/translational control signals. These methods include in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination/genetic recombination. See, for example, the techniques described in Sambrook & Russell, Molecular Cloning: A Laboratory Manual, 3rd Edition, Cold Spring Harbor Laboratory, N.Y. (2001 ) and Ausubel et al., Current Protocols in Molecular Biology (Greene Publishing Associates and Wiley Interscience, N.Y. (1989 ). Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers.
  • CAT chloramphenicol transferase
  • the vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host.
  • Suitable prokaryotic hosts for transformation include E. coli, Bacillus subtilis, Salmonella typhimurium and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus, although others may also be employed as a matter of choice.
  • the present invention provides host cells genetically engineered to contain the polynucleotides of the invention.
  • host cells may contain nucleic acids of the invention introduced into the host cell using known transformation, transfection or infection methods.
  • the present invention also provides host cells genetically engineered to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of the polynucleotides in the cell.
  • the present invention further provides host cells containing the vectors of the present invention, wherein the nucleic acid has been introduced into the host cell using known transformation, transfection or infection methods.
  • the host cell can be a eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell.
  • Introduction of the recombinant construct into the host cell can be effected, for example, by calcium phosphate transfection, DEAE, dextran mediated transfection, or electroporation ( Davis, L. et al., Basic Methods in Molecular Biology (1986 )). Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention.
  • Any host/vector system can be used to express one or more of the proteins products of the biomarkers of the invention including those listed in Table 3 and/or Table 13 .
  • Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook et al., in Molecular Cloning: A Laboratory, Manual, Second Edition, Cold Spring Harbor, New York (1989 ), the disclosure of which is incorporated herein by reference in its entirety.
  • the most preferred host cells are those which do not normally express the particular polypeptide or which expresses the polypeptide at low natural level.
  • the host cells are engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination.
  • gene targeting can be used to replace a gene's existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods.
  • regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences.
  • the host of the present invention may also be a yeast or other fungi.
  • yeast a number of vectors containing constitutive or inducible promoters may be used.
  • Ausubel et al. eds
  • Current Protocols in Molecular Biology Vol. 2, Greene Publish. Assoc. & Wiley Interscience, Ch. 13 (1988 ); Grant et al., 1987, "Expression and Secretion Vectors for Yeast", Methods Enzymol. 153:516-544 ; Glover, DNA Cloning, Vol. II, IRL Press, Wash., D.C., Ch. 3 (1986 ); Bitter, 1987, "Heterologous Gene Expression in Yeast", Methods Enzymol. 152:673-684 ; and Strathern et al. (eds), The Molecular Biology of the Yeast Saccharomyces, Cold Spring Harbor Press, Vols. I and II (1982 ).
  • Mammalian expression vectors will comprise an origin of replication, a suitable promoter and also any necessary ribosome-binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking nontranscribed sequences.
  • Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents.
  • Recombinant polypeptides produced in bacterial culture are usually isolated by initial extraction from cell pellets, followed by one or more salting-out, aqueous ion exchange or size exclusion chromatography steps.
  • the template nucleic acid also encodes a polypeptide tag, e.g., penta- or hexa-histidine.
  • the present invention provides methods of identifying compounds that bind to the products of the biomarkers of the invention.
  • the present invention also provides methods for identifying compounds that modulate the expression and/or activity of the products of the biomarkers of the invention.
  • the compounds identified via such methods are useful for the development of one or more animal models to study colorectal pathology including polyps or one or more subtypes of polyps. Further, the compounds identified via such methods are useful as lead compounds in the development of prophylactic and therapeutic compositions for prevention, treatment, and/or amelioration of one or more colorectal pathologies including one or more polyps or one or more subtypes of polyps.
  • Such methods are particularly useful in that the effort and great expense involved in testing potential prophylactics and therapeutics in vivo is efficiently focused on those compounds identified via the in vitro and ex vivo methods described herein.
  • the present invention provides a method for identifying a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies said method comprising: (a) contacting a cell expressing a protein products of one or more biomarkers of the invention or a fragment thereof, or RNA products of one or more biomarkers of the invention or a fragment thereof with a test compound; and (b) determining the ability of the test compound to bind to the protein products, protein fragment, RNA products, or RNA portion so that if a compound binds to the protein products, protein fragment, RNA products, RNA portions, a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies is identified.
  • the cell for example, can be a prokaryotic cell, yeast cell, viral cell or a cell of mammalian origin. Determining the ability of the test compound to bind to the protein products, protein fragment, RNA products, or RNA portion can be accomplished, for example, by coupling the test compound with a radioisotope or enzymatic label such that binding of the test compound to the protein products, protein fragment, RNA products, or RNA portion can be determined by detecting the labeled compound in a complex.
  • test compounds can be labeled with 125 I 35 S, 14 C, or 3 H, either directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting.
  • the assay comprises contacting a cell which expresses a protein products of one or more biomarkers of the invention or a fragment thereof, or a RNA products of one or more biomarkers of the invention or a fragment thereof, with a known compound which binds the protein products, protein fragment, RNA products, or RNA portion to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the protein products, protein fragment, RNA products, or RNA portion, wherein determining the ability of the test compound to interact with the protein products, protein fragment, RNA products, or RNA portion comprises determining the ability of the test compound to preferentially bind to the protein products, protein fragment, RNA products, or RNA portion as compared to the known compound.
  • a protein products of a biomarker of the invention or a fragment thereof, or a target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
  • a biotinylated protein products of a biomarker of the invention or a target molecule can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals; Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
  • antibodies reactive with a protein products of a biomarker of the invention or a fragment thereof can be derivatized to the wells of the plate, and protein trapped in the wells by antibody conjugation.
  • Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with a protein products of a biomarker of the invention, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with a protein products of a biomarker of the invention or a fragment thereof, or target molecule.
  • the interaction or binding of a protein products of a biomarker of the invention or a fragment thereof to a test compound can also be determined using such proteins or protein fragments as "bait proteins" in a two-hybrid assay or three hybrid assay (see, e.g., U.S. Patent No. 5,283,317 ; Zervos et al. (1993) Cell 72:223-232 ; Madura et al. (1993) J. Biol. Chem. 268:12046-12054 ; Bartel et al. (1993) Bio/Techniques 14:920-924 ; Iwabuchi et al. (1993) Oncogene 8:1693-1696 ; and International Publication No. WO 94/10300 ).
  • the present invention provides a method for identifying a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies, said method comprising: (a) contacting a cell expressing a protein or RNA products of one or more biomarkers of the invention with a test compound; (b) determining the amount of the protein or RNA products present in (a); and (c) comparing the amount in (a) to that present in a corresponding control cell that has not been contacted with the test compound, so that if the amount of the protein or RNA products is altered relative to the amount in the control, a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies is identified.
  • the expression level(s) is altered by 5%, 10%, 15%, 25%, 30%, 40%, 50%, 5 to 25%, 10 to 30%, at least 1 fold, at least 1.5 fold, at least 2 fold, 4 fold, 5 fold, 10 fold, 25 fold, 1 to 10 fold, or 5 to 25 fold relative to the expression level in the control as determined by utilizing an assay described herein (e.g., a microarray or QRT-PCR) or an assay well known to one of skill in the art.
  • an assay described herein e.g., a microarray or QRT-PCR
  • such a method comprises determining the amount of the protein or RNA products of at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, 1 to 3, 1 to 5, 1-8, all or any combination of the biomarkers of the invention present in the cell and comparing the amounts to those present in the control.
  • intestinal cells are isolated from a "normal" individual, or an individual with one or more colorectal pathologies and are incubated in the presence and absence of a test compound for varying amounts of time (i.e., 30 min, 1 hr, 5 hr, 24 hr, 48 hr and 96 hrs).
  • a clone of the full sequence of a biomarker of the invention or functional portion thereof is used to transfect the cells.
  • the transfected cells are cultured for varying amounts of time (i.e., 1, 2, 3, 5, 7, 10, or 14 days) in the presence or absence of test compound.
  • target nucleic acid samples are prepared from the cells and hybridized to a nucleic acid probe corresponding to a nucleic acid sequence which are differentially expressed in individuals with one or more colorectal pathologies.
  • the nucleic acid probe is labeled, for example, with a radioactive label, according to methods well-known in the art and described herein.
  • Hybridization is carried out by northern blot, for example as described in Ausubel et al., supra or Sambrook et al., supra ) .
  • the present invention also provides a method for identifying a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies, said method comprises: (a) contacting a cell-free extract (e.g., an intestinal cell extract) with a nucleic acid sequence encoding a protein or RNA products of one or more biomarkers of the invention and a test compound; (b) determining the amount of the protein or RNA product present in (a); and (c) comparing the amount(s) in (a) to that present to a corresponding control that has not been contacted with the test compound, so that if the amount of the protein or RNA product is altered relative to the amount in the control, a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies is identified.
  • a cell-free extract e.g., an intestinal cell extract
  • a nucleic acid sequence encoding a protein or RNA products of one or more biomarkers of the invention and
  • the expression level(s) is altered by 5%, 10%, 15%, 25%, 30%, 40%, 50%, 5 to 25%, 10 to 30%, at least 1 fold, at least 1.5 fold, at least 2 fold, 4 fold, 5 fold, 10 fold, 25 fold, 1 to 10 fold, or 5 to 25 fold relative to the expression level in the control sample determined by utilizing an assay described herein (e.g., a microarray or QRT-PCR) or an assay well known to one of skill in the art.
  • an assay described herein e.g., a microarray or QRT-PCR
  • such a method comprises determining the amount of a protein or RNA product of at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, 1 to 3, 1 to 5, 1-8, all or any combination of the biomarkers of the invention present in the extract and comparing the amounts to those present in the control.
  • kits comprise materials and reagents required for measuring the expression of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8 protein or RNA products of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, all or any combination of the biomarkers of the invention.
  • kits may further comprise one or more additional reagents employed in the various methods, such as: (1) reagents for purifying RNA from blood; (2) primers for generating test nucleic acids; (3) dNTPs and/or rNTPs (either premixed or separate), optionally with one or more uniquely labeled dNTPs and/or rNTPs (e.g., biotinylated or Cy3 or Cy5 tagged dNTPs); (4) post synthesis labeling reagents, such as chemically active derivatives of fluorescent dyes; (5) enzymes, such as reverse transcriptases, DNA polymerases, and the like; (6) various buffer mediums, e.g., hybridization and washing buffers; (7) labeled probe purification reagents and components, like spin columns, etc.; and (8) protein purification reagents; (9) signal generation and detection reagents, e.g., streptavidin-alkaline phosphatase conjug
  • kits are QRT-PCR kits.
  • the kits are nucleic acid arrays and protein arrays.
  • Such kits according to the subject invention will at least comprise an array having associated protein or nucleic acid members of the invention and packaging means therefore.
  • the protein or nucleic acid members of the invention may be prepackaged onto an array.
  • kits for measuring a RNA product of a biomarker of the invention comprise materials and reagents that are necessary for measuring the expression of the RNA product.
  • a microarray or QRT-PCR kit may be used and contain only those reagents and materials necessary for measuring the levels of RNA products of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, all or any combination of the biomarkers of the invention.
  • the kits can comprise materials and reagents that are not limited to those required to measure the levels of RNA products of 1, 2, 3, 4, 5, 6, 7, 8 all or any combination of the biomarkers of the invention.
  • a microarray kit may contain reagents and materials necessary for measuring the levels of RNA products 1,2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention, in addition to reagents and materials necessary for measuring the levels of the RNA products of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, or more genes other than the biomarkers of the invention.
  • a microarray or QRT-PCR kit contains reagents and materials necessary for measuring the levels of RNA products of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, all or any combination of the biomarkers of the invention, and 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 300, 350, 400, 450, or more genes that are not biomarkers of the invention, or 1-10, 1-100, 1-150, 1-200, 1-300, 1-400, 1-500, 1-1000, 25-100, 25-200, 25-300, 25-400, 25-500, 25-1000, 100-150, 100-200, 100-300, 100-400, 100-500, 100-1000 or 500-1000 or more genes that are not biomarkers of the invention.
  • the kits generally comprise probes attached or localized to a support surface.
  • the probes may be labeled with a detectable label.
  • the probes are specific for the 5' region, the 3' region, the internal coding region, an exon(s), an intron(s), an exon junction(s), or an exon-intron junction(s), of 1, 2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention.
  • the microarray kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.
  • kits may also comprise hybridization reagents and/or reagents necessary for detecting a signal produced when a probe hybridizes to a target nucleic acid sequence.
  • the materials and reagents for the microarray kits are in one or more containers. Each component of the kit is generally in its own a suitable container.
  • kits generally comprise pre-selected primers specific for particular RNA products (e.g., an exon(s), an intron(s), an exon junction(s), and an exon-intron junction(s)) of 1, 2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention.
  • the QRT-PCR kits may also comprise enzymes suitable for reverse transcribing and/or amplifying nucleic acids (e.g., polymerases such as Taq, enzymes such as reverse transcriptase etc.), and deoxynucleotides and buffers needed for the reaction mixture for reverse transcription and amplification.
  • the QRT-PCR kits may also comprise biomarker specific sets of primers specific for 1,2,3,4,5, 6, 7, 8, all or any combination of the biomarkers of the invention.
  • the QRT-PCR kits may also comprise biomarker specific probes which are specific for the sequences amplified from 1, 2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention using the biomarker specific sets of primers.
  • the probes may or may not be labeled with a detectable label (e.g., a fluorescent label).
  • a detectable label e.g., a fluorescent label
  • a different detectable label e.g. FAM or HEX
  • Each component of the QRT-PCR kit is generally in its own suitable container.
  • these kits generally comprise distinct containers suitable for each individual reagent, enzyme, primer and probe.
  • the QRT-PCR kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.
  • the kit can comprise, for example: (1) a first antibody (which may or may not be attached to a support) which binds to protein of interest (e.g., a protein products of 1, 2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention); and, optionally, (2) a second, different antibody which binds to either the protein, or the first antibody and is conjugated to a detectable label (e.g., a fluorescent label, radioactive isotope or enzyme).
  • the antibody-based kits may also comprise beads for conducting an immunoprecipitation. Each component of the antibody-based kits is generally in its own suitable container. Thus, these kits generally comprise distinct containers suitable for each antibody.
  • the antibody-based kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.
  • Reporter gene-based assays may also be conducted to identify a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies.
  • the present invention provides a method for identifying a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies, said method comprising: (a) contacting a compound with a cell expressing a reporter gene construct comprising a reporter gene operably linked to a regulatory element of a biomarker of the invention (e.g., a promoter/enhancer element); (b) measuring the expression of said reporter gene; and (c) comparing the amount in (a) to that present in a corresponding control cell that has not been contacted with the test compound, so that if the amount of expressed reporter gene is altered relative to the amount in the control cell, a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies is identified.
  • reporter genes refer to a nucleotide sequence encoding a RNA transcript or protein that is readily detectable either by its presence (by, e.g., RT-PCR, Northern blot, Western Blot, ELISA, etc .) or activity.
  • Non-limiting examples of reporter genes are listed in Table 10. Reporter genes may be obtained and the nucleotide sequence of the elements determined by any method well-known to one of skill in the art.
  • the nucleotide sequence of a reporter gene can be obtained, e.g., from the literature or a database such as GenBank.
  • a polynucleotide encoding a reporter gene may be generated from nucleic acid from a suitable source. If a clone containing a nucleic acid encoding a particular reporter gene is not available, but the sequence of the reporter gene is known, a nucleic acid encoding the reporter gene may be chemically synthesized or obtained from a suitable source (e.g., a cDNA library, or a cDNA library generated from, or nucleic acid, preferably poly A+ RNA, isolated from, any tissue or cells expressing the reporter gene) by PCR amplification.
  • a suitable source e.g., a cDNA library, or a cDNA library generated from, or nucleic acid, preferably poly A+ RNA, isolated from, any tissue or cells expressing the reporter gene
  • nucleotide sequence of a reporter gene may be manipulated using methods well-known in the art for the manipulation of nucleotide sequences, e.g., recombinant DNA techniques, site directed mutagenesis, PCR, etc.
  • dextran-mediated transfection dextran-mediated transfection
  • calcium phosphate mediated transfection polybrene mediated transfection
  • protoplast fusion protoplast fusion
  • electroporation electroporation
  • encapsulation of the nucleic acid in liposomes and direct microinjection of the nucleic acid into nuclei.
  • the cell-free extract may be isolated from cells of any species origin.
  • the cell-free translation extract may be isolated from human cells, cultured mouse cells, cultured rat cells, Chinese hamster ovary (CHO) cells, Xenopus oocytes, rabbit reticulocytes, wheat germ, or rye embryo (see, e.g., Krieg & Melton, 1984, Nature 308:203 and Dignam et al., 1990 Methods Enzymol. 182:194-203 ).
  • the cell-free translation extract e.g., rabbit reticulocyte lysates and wheat germ extract
  • the cell-free extract can be purchased from, e.g., Promega, (Madison, WI).
  • the cell-free extract is an extract isolated from human cells.
  • the human cells are HeLa cells, lymphocytes, or intestinal cells or cell lines.
  • the present invention provides methods of identifying compounds to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies, comprising methods for identifying compounds that modulate the activity of a protein products of one or more biomarkers of the invention.
  • Such methods can comprise: (a) contacting a cell expressing a protein products of one or more biomarkers of the invention with a test compound; (b) determining the activity level of the protein products; and (c) comparing the activity level to that in a corresponding control cell that has not been contacted with the test compound, so that if the level of activity in (a) is altered relative to the level of activity in the control cell, a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies is identified.
  • the activity level(s) is altered by 5%, 10%, 15%, 25%, 30%, 40%, 50%, 5 to 25%, 10 to 30%, at least 1 fold, at least 1.5 fold, at least 2 fold, 4 fold, 5 fold, 10 fold, 25 fold, 1 to 10 fold, or 5 to 25 fold relative to the activity level in the control as determined by utilizing an assay described herein (e.g., a microarray or QRT-PCR) or an assay well known to one of skill in the art.
  • an assay described herein e.g., a microarray or QRT-PCR
  • such a method comprises determining the activity level of a protein products of at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 15, 1 to 5, 1-10, 5-10, 5-15, or 10-15, or more, or all or any combination of the biomarkers of the invention present in the cell and comparing the activity levels to those present in the control.
  • the present invention provides methods of identifying compounds to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies, comprising: (a) contacting a cell-free extract with a nucleic acid encoding a protein products of one or more biomarkers of the invention and a test compound; (b) determining the activity level of the protein products; and (c) comparing the activity level to that in a corresponding control that has not been contacted with the test compound, so that if the level of activity in (a) is altered relative to the level of activity in the control, a compound to be tested for an ability to prevent, treat, or ameliorate one or more colorectal pathologies is identified.
  • the activity level(s) is altered by 5%, 10%, 15%, 25%, 30%, 40%, 50%, 5 to 25%, 10 to 30%, at least 1 fold, at least 1.5 fold, at least 2 fold, 4 fold, 5 fold, 10 fold, 25 fold, 1 to 10 fold, or 5 to 25 fold relative to the activity level in the control as determined by utilizing an assay described herein (e.g., a microarray or QRT-PCR) or an assay well known to one of skill in the art.
  • an assay described herein e.g., a microarray or QRT-PCR
  • such a method comprises determining the activity level of a protein products of at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, 1 to 3, 1 to 5,1-8 all or any combination of the biomarkers of the invention present in the sample and comparing the activity levels to those present in the control.
  • Standard techniques can be utilized to determine the level of activity of a protein products of a biomarker of the invention. Activities of protein productss of biomarkers of the invention that can be determined using techniques well known in the art.
  • the compounds can be further investigated.
  • the compounds identified via the present methods can be further tested in vivo in accepted animal models of polyp formation. Further, the compounds identified via the methods can be analyzed with respect to their specificity. Techniques for such additional compound investigation are well known to one of skill in the art.
  • the effect of a lead compound can be assayed by measuring the cell growth or viability of the target cell.
  • assays can be carried out with representative cells of cell types involved in polyp formation (e.g., intestinal cells; cells isolated from different portions of the gastrointestinal system and the like).
  • representative cells of cell types involved in polyp formation e.g., intestinal cells; cells isolated from different portions of the gastrointestinal system and the like.
  • a lead compound may be screened using cells of a cell line.
  • RNA e.g., mRNA
  • activity can be determined by any method well known in the art.
  • protein can be quantitated by known immunological based methods such as Western blotting or immunoprecipitation using commercially available antibodies.
  • mRNA can be quantitated using methods that are well known and routine in the art, for example, using northern analysis, RNase protection, the polymerase chain reaction in connection with the reverse transcription.
  • Cell viability can be assessed by using trypan-blue staining or other cell death or viability markers known in the art.
  • the level of cellular ATP is measured to determined cell viability. Differentiation can be assessed, for example, visually based on changes in morphology.
  • Compounds can be tested in suitable animal model systems prior to use in humans.
  • animal model systems include but are not limited to rats, mice, chicken, cows, monkeys, pigs, dogs, rabbits, etc. Any animal system well-known in the art may be used.
  • compounds are tested in a mouse model.
  • Compounds can be administered repeatedly.
  • Accepted animal models can be utilized to determine the efficacy of the compounds identified via the methods described above for the prevention, treatment, and/or amelioration of one or more colorectal pathologies.
  • the toxicity and/or efficacy of a compound identified in accordance with the invention can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD 50 (the dose lethal to 50% of the population) and the ED 50 (the dose therapeutically effective in 50% of the population).
  • Cells and cell lines that can be used to assess the cytotoxicity of a compound identified in accordance with the invention include, but are not limited to, peripheral blood mononuclear cells (PBMCs), Caco-2 cells, and Huh7 cells.
  • PBMCs peripheral blood mononuclear cells
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD 50 /ED 50 .
  • a compound identified in accordance with the invention that exhibits large therapeutic indices is preferred. While a compound identified in accordance with the invention that exhibits toxic side effects may be used, care should be taken to design a delivery system that targets such agents to the site of affected tissue in order to minimize potential damage to uninfected
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage of a compound identified in accordance with the invention for use in humans.
  • the dosage of such agents lies preferably within a range of circulating concentrations that include the ED 50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 50 (i.e., the concentration of the compound that achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC 50 i.e., the concentration of the compound that achieves a half-maximal inhibition of symptoms
  • levels in plasma may be measured, for example, by high performance liquid chromatography.
  • the compounds which display the desired biological activity can be used as lead compounds for the development or design of congeners or analogs having useful pharmacological activity.
  • molecular modeling techniques can be used to design variants of the compound that can be more effective.
  • molecular modeling systems are the CHARM and QUANTA programs (Polygen Corporation, Waltham, MA).
  • CHARM performs the energy minimization and molecular dynamics functions.
  • QUANTA performs the construction, graphic modelling and analysis of molecular structure. QUANTA allows interactive construction, modification, visualization, and analysis of the behavior of molecules with each other.
  • Compounds that can be tested and identified methods described herein can include, but are not limited to, compounds obtained from any commercial source, including Aldrich (1001 West St. Paul Ave., Milwaukee, WI 53233), Sigma Chemical (P.O. Box 14508, St. Louis, MO 63178), Fluka Chemie AG (Industriestrasse 25, CH-9471 Buchs, Switzerland (Fluka Chemical Corp.
  • Synthetic compound libraries are commercially available from a number of companies including Maybridge Chemical Co. (Trevillet, Cornwall, UK), Comgenex (Princeton, NJ), Brandon Associates (Merrimack, NH), and Microsource (New Milford, CT).
  • a rare chemical library is available from Aldrich (Milwaukee, WI). Combinatorial libraries are available and are prepared.
  • libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available from e.g., Pan Laboratories (Bothell, WA) or MycoSearch (NC), or are readily produceable by methods well known in the art. Additionally, natural and synthetically produced libraries and compounds are readily modified through conventional chemical, physical, and biochemical means.
  • libraries screened using the methods of the present invention can comprise a variety of types of compounds.
  • libraries that can be screened in accordance with the methods of the invention include, but are not limited to, peptoids; random biooligomers; diversomers such as hydantoins, benzodiazepines and dipeptides; vinylogous polypeptides; nonpeptidal peptidomimetics; oligocarbamates; peptidyl phosphonates; peptide nucleic acid libraries; antibody libraries; carbohydrate libraries; and small molecule libraries (in some embodiments, small organic molecule libraries).
  • the compounds in the libraries screened are nucleic acid or peptide molecules.
  • Combinatorial libraries are themselves commercially available
  • libraries may be commercially obtained from, e.g., Specs and BioSpecs B.V. (Rijswijk, The Netherlands), Chembridge Corporation (San Diego, CA ), Contract Service Company (Dolgoprudny, Moscow Region, Russia), Comgenex USA Inc. (Princeton, NJ), Maybridge Chemicals Ltd. (Cornwall PL34 OHW, United Kingdom), Asinex (Moscow, Russia), ComGenex (Princeton, New Jersey), Ru, Tripos, Inc. (St. Louis, Missouri), ChemStar, Ltd (Moscow, Russia), 3D Pharmaceuticals (Exton, Pennsylvania), and Martek Biosciences (Columbia, Maryland).
  • the invention also provides methods of preventing, treating, or ameliorating one or more colorectal pathologies, said methods comprising administering to a subject in need thereof one or more of the compounds identified utilizing the screening methods described herein, and one or more other therapies (e.g., prophylactic or therapeutic agents and surgery).
  • therapies e.g., prophylactic or therapeutic agents and surgery.
  • such therapies are currently being used, have been used or are known to be useful in the prevention, treatment, or amelioration of one or more colorectal pathologies (including, but not limited to the prophylactic or therapeutic agents listed herein).
  • the therapies (e.g., prophylactic or therapeutic agents) of the combination therapies of the invention can be administered sequentially or concurrently.
  • PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup, 1996, supra ) .
  • the synthesis of PNA-DNA chimeras can be performed as described in Hyrup, 1996, supra, and Finn et al., 1996, Nucleic Acids Res. 24(17):3357-63 .
  • a DNA chain can be synthesized on a support using standard phosphoramidite coupling chemistry and modified nucleoside analogs.
  • Antibodies can also be produced by a transgenic animal.
  • human antibodies can be produced using transgenic mice which are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes.
  • the human heavy and light chain immunoglobulin gene complexes may be introduced randomly or by homologous recombination into mouse embryonic stem cells.
  • the human variable region, constant region, and diversity region may be introduced into mouse embryonic stem cells in addition to the human heavy and light chain genes.
  • the mouse heavy and light chain immunoglobulin genes may be rendered non-functional separately or simultaneously with the introduction of human immunoglobulin loci by homologous recombination. In particular, homozygous deletion of the J H region prevents endogenous antibody production.
  • U.S. Patent No. 5,849,992 describes a method of expressing an antibody in the mammary gland of a transgenic mammal.
  • a transgene is constructed that includes a milk-specific promoter and nucleic acids encoding the antibody of interest and a signal sequence for secretion.
  • the milk produced by females of such transgenic mammals includes, secreted-therein, the antibody of interest.
  • the antibody can be purified from the milk, or for some applications, used directly.
  • the constant domain is a complement fixing constant domain where it is desired that the humanized antibody exhibit cytotoxic activity, and the class is typically IgG 1 . Where such cytotoxic activity is not desirable, the constant domain may be of the IgG 2 class.
  • the humanized antibody may comprise sequences from more than one class or isotype, and selecting particular constant domains to optimize desired effector functions is within the ordinary skill in the art.
  • the framework and CDR regions of a humanized antibody need not correspond precisely to the parental sequences, e.g., the donor CDR or the consensus framework may be mutagenized by substitution, insertion or deletion of at least one residue so that the CDR or framework residue at that site does not correspond to either the consensus or the import antibody. Such mutations, however, will not be extensive.
  • Single domain antibodies for example, antibodies lacking the light chains, can be produced by methods well-known in the art. See Riechmann et al., 1999, J. Immuno. 231:25-38 ; Nuttall et al., 2000, Curr. Pharm. Biotechnol. 1(3):253-263 ; Muylderman, 2001, J. Biotechnol. 74(4):277302 ; U.S. Patent No. 6,005,079 ; and International Publication Nos. WO 94/04678 , WO 94/25591 , and WO 01/44301 , each of which is incorporated herein by reference in its entirety.
  • monoclonal antibodies are produced in mammalian cells.
  • Preferred mammalian host cells for expressing the clone antibodies or antigen-binding fragments thereof include Chinese Hamster Ovary (CHO cells) (including dhfr- CHO cells, described in Urlaub and Chasin (1980, Proc. Natl. Acad. Sci. USA 77:4216-4220 ), used with a DHFR selectable marker, e.g., as described in Kaufman and Sharp (1982, Mol. Biol.
  • lymphocytic cell lines e.g., NSO myeloma cells and SP2 cells, COS cells, and a cell from a transgenic animal, e.g., a transgenic mammal.
  • the cell is a mammary epithelial cell.
  • an antibody molecule may be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. Further, the antibodies or fragments thereof may be fused to heterologous polypeptide sequences known in the art to facilitate purification.
  • a composition of the invention comprises nucleic acid sequences encoding one or more antibodies that specifically bind to one or more protein products of one or more biomarkers of the invention, said nucleic acid sequences being part of expression vectors that express one or more antibodies in a suitable host.
  • nucleic acid sequences have promoters operably linked to the antibodies, said promoter being inducible or constitutive, and, optionally, tissue-specific.
  • Delivery of the nucleic acids into a patient may be either direct, in which case the patient is directly exposed to the nucleic acid or nucleic acid-carrying vectors, or indirect, in which case, cells are first transformed with the nucleic acids in vitro, then transplanted into the patient. These two approaches are known, respectively, as in vivo or ex vivo gene therapy.
  • microparticle bombardment e.g., a gene gun; Biolistic, Dupont
  • coating lipids or cell-surface receptors or transfecting agents, encapsulation in liposomes, microparticles, or microcapsules, or by administering them in linkage to a peptide which is known to enter the nucleus, by administering it in linkage to a ligand subject to receptor-mediated endocytosis (see, e.g., Wu and Wu, 1987, J. Biol. Chem. 262:4429-4432 ) (which can be used to target cell types specifically expressing the receptors), etc.
  • nucleic acid-ligand complexes can be formed in which the ligand comprises a fusogenic viral peptide to disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation.
  • the nucleic acid can be targeted in vivo for cell specific uptake and expression, by targeting a specific receptor (see, e.g., International Publication Nos. WO 92/06180 dated April 16, 1992 (Wu et al. ); WO 92/22635 dated December 23, 1992 (Wilson et al. ); WO92/20316 dated November 26, 1992 (Findeis et al. ); WO 93/14188 dated July 22, 1993 (Clarke et al.
  • a retroviral vector can be used. These retroviral vectors have been modified to delete retroviral sequences that are not necessary for packaging of the viral genome and integration into host cell DNA.
  • the nucleic acid sequences encoding the antibodies of interest, or proteins of interest or fragments thereof to be used in gene therapy are cloned into one or more vectors, which facilitates delivery of the gene into a patient. More detail about retroviral vectors can be found in Boesen et al., 1994, Biotherapy 6:291-302 , which describes the use of a retroviral vector to deliver the mdr1 gene to hematopoietic stem cells in order to make the stem cells more resistant to chemotherapy.
  • Adenoviruses are other viral vectors that can be used in gene therapy. Adenoviruses are especially attractive vehicles for delivering genes to respiratory epithelia. Adenoviruses naturally infect respiratory epithelia where they cause a mild disease. Other targets for adenovirus-based delivery systems are liver, the central nervous system, endothelial cells, and muscle. Adenoviruses have the advantage of being capable of infecting non-dividing cells. Kozarsky and Wilson, 1993, Current Opinion in Genetics and Development 3:499-503 present a review of adenovirus-based gene therapy.
  • adenovirus vectors are used.
  • Adeno-associated virus has also been proposed for use in gene therapy ( Walsh et al., 1993, Proc. Soc. Exp. Biol. Med. 204:289-300 ; U.S. Patent No. 5,436,146 ).
  • Another approach to gene therapy involves transferring a gene to cells in tissue culture by such methods as electroporation, lipofection, calcium phosphate mediated transfection, or viral infection.
  • the method of transfer includes the transfer of a selectable marker to the cells. The cells are then placed under selection to isolate those cells that have taken up and are expressing the transferred gene. Those cells are then delivered to a patient.
  • the nucleic acid is introduced into a cell prior to administration in vivo of the resulting recombinant cell.
  • introduction can be carried out by any method known in the art, including but not limited to transfection, electroporation, microinjection, infection with a viral or bacteriophage vector containing the nucleic acid sequences, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer, spheroplast fusion, etc.
  • Numerous techniques are known in the art for the introduction of foreign genes into cells (see, e.g., Loeffler and Behr, 1993, Meth. Enzymol. 217:599-618 ; Cohen et al., 1993, Meth. Enzymol.
  • the technique should provide for the stable transfer of the nucleic acid to the cell, so that the nucleic acid is expressible by the cell and preferably heritable and expressible by its cell progeny.
  • the resulting recombinant cells can be delivered to a patient by various methods known in the art.
  • Recombinant blood cells e.g., hematopoietic stem or progenitor cells
  • intestinal cells are preferably administered intravenously.
  • the amount of cells envisioned for use depends on the desired effect, patient state, etc., and can be determined by one skilled in the art.
  • Cells into which a nucleic acid can be introduced for purposes of gene therapy encompass any desired, available cell type, and include but are not limited to epithelial cells, endothelial cells, keratinocytes, intestinal cells, fibroblasts, muscle cells, hepatocytes; blood cells such as T lymphocytes, B lymphocytes, monocytes, macrophages, neutrophils, eosinophils, megakaryocytes, granulocytes; various stem or progenitor cells, in particular hematopoietic stem or progenitor cells, e.g., as obtained from bone marrow, umbilical cord blood, peripheral blood, fetal liver, etc.
  • the cell used for gene therapy is autologous to the patient.
  • nucleic acid sequences encoding antibodies of interest, or proteins of interest or fragments thereof are introduced into the cells such that they are expressible by the cells or their progeny, and the recombinant cells are then administered in vivo for therapeutic effect.
  • stem or progenitor cells are used. Any stem and/or progenitor cells which can be isolated and maintained in vitro can potentially be used in accordance with this embodiment of the present invention (see, e.g., International Publication No. WO 94/08598, dated April 28, 1994 ; Stemple and Anderson, 1992, Cell 71:973-985 ; Rheinwald, 1980, Meth. Cell Bio. 21A:229 ; and Pittelkow and Scott, 1986, Mayo Clinic Proc. 61:771 ).
  • Promoters that may be used to control the expression of nucleic acid sequences encoding antibodies of interest, proteins of interest or fragments thereof may be constitutive, inducible or tissue- specific.
  • Non-limiting examples include the SV40 early promoter region ( Bernoist and Chambon, 1981, Nature 290:304-310 ), the promoter contained in the 3' long terminal repeat of Rous sarcoma virus ( Yamamoto, et al., 1980, Cell 22:787-797 ), the herpes thymidine kinase promoter ( Wagner et al., 1981, Proc. Natl. Acad. Sci.
  • promoter of the photosynthetic enzyme ribulose biphosphate carboxylase ( Herrera-Estrella et al., 1984, Nature 310:115-120 ); promoter elements from yeast or other fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, alkaline phosphatase promoter, and the following animal transcriptional control regions, which exhibit tissue specificity and have been utilized in transgenic animals: elastase I gene control region which is active in pancreatic acinar cells ( Swift et al., 1984, Cell 38:639-646 ; Omitz et al., 1986, Cold Spring Harbor Symp.
  • beta-globin gene control region which is active in myeloid cells ( Mogram et al., 1985, Nature 315:338-340 ; Kollias et al., 1986, Cell 46:89-94 ; myelin basic protein gene control region which is active in oligodendrocyte cells in the brain ( Readhead et al., 1987, Cell 48:703-712 ); myosin light chain-2 gene control region which is active in skeletal muscle ( Sani, 1985, Nature 314:283-286 ), and gonadotropic releasing hormone gene control region which is active in the hypothalamus ( Mason et al., 1986, Science 234:1372-1378 ).
  • Biologically active compounds identified using the methods of the invention or a pharmaceutically acceptable salt thereof can be administered to a patient, in some embodiments a mammal, including a human, having one or more colorectal pathologies.
  • a compound or pharmaceutically acceptable salt thereof is administered to a patient, in some embodiments a mammal, including a human, having one or more colorectal pathologies.
  • a compound or a pharmaceutically acceptable salt thereof is administered to a patient, in some embodiments a mammal, including a human, as a preventative measure against one or more colorectal pathologies.
  • the patient may be a child, an adult or elderly, wherein a "child” is a subject between the ages of 24 months of age and 18 years of age, an "adult” is a subject 18 years of age or older, and “elderly” is a subject 65 years of age or older.
  • the compound or a pharmaceutically acceptable salt thereof is administered as component of a composition that optionally comprises a pharmaceutically acceptable vehicle.
  • the composition can be administered orally, or by any other convenient route, for example, by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal, and intestinal mucosa, etc .) and may be administered together with another biologically active agent. Administration can be systemic or local.
  • Various delivery systems are known, e.g., encapsulation in liposomes, microparticles, microcapsules, capsules, etc., and can be used to administer the compound and pharmaceutically acceptable salts thereof.
  • Methods of administration include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, oral, sublingual, intranasal, intracerebral, intravaginal, transdermal, rectally, by inhalation, or topically, particularly to the ears, nose, eyes, or skin.
  • the mode of administration is left to the discretion of the practitioner. In most instances, administration will result in the release of the compound or a pharmaceutically acceptable salt thereof into the bloodstream.
  • This may be achieved, for example, and not by way of limitation, by local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.
  • a compound is administered locally to one or more sections of the gastrointestinal system.
  • Intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir.
  • Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent, or via perfusion in a fluorocarbon or synthetic pulmonary surfactant.
  • the compound and pharmaceutically acceptable salts thereof can be formulated as a suppository, with traditional binders and vehicles such as triglycerides.
  • the compound and pharmaceutically acceptable salts thereof can be delivered in a vesicle, in particular a liposome (see Langer, 1990, Science 249:1527-1533 ; Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989 ); Lopez-Berestein, ibid., pp. 317-327 ; see generally ibid. ).
  • a liposome see Langer, 1990, Science 249:1527-1533 ; Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989 ); Lopez-Berestein, ibid., pp. 317-327 ; see generally ibid. ).
  • the compound and pharmaceutically acceptable salts thereof can be delivered in a controlled release system (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984 )).
  • a controlled release system see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984 )).
  • Other controlled-release systems discussed in the review by Langer, 1990, Science 249:1527-1533 may be used.
  • a pump may be used (see Langer, supra; Sefton, 1987, CRC Crit. Ref. Biomed. Eng. 14:201 ; Buchwald et al., 1980, Surgery 88:507 ; Saudek et al., 1989, N. Engl. J. Med. 321:574 ).
  • polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Florida (1974 ); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984 ); Ranger and Peppas, 1983, J. Macromol. Sci. Rev. Macromol. Chem. 23:61 ; see also Levy et al., 1985, Science 228:190 ; During et al., 1989, Ann. Neurol. 25:351 ; Howard et al., 1989, J. Neurosurg. 71:105 ).
  • a controlled-release system can be placed in proximity of a target RNA of the compound or a pharmaceutically acceptable salt thereof, thus requiring only a fraction of the systemic dose.
  • compositions suitable for administration typically comprise the active compound and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
  • the invention includes methods for preparing pharmaceutical compositions for modulating the expression or activity of a polypeptide or nucleic acid of interest. Such methods comprise formulating a pharmaceutically acceptable carrier with an agent that modulates expression or activity of a polypeptide or nucleic acid of interest. Such compositions can further include additional active agents. Thus, the invention further includes methods for preparing a pharmaceutical composition by formulating a pharmaceutically acceptable carrier with an agent that modulates expression or activity of a polypeptide or nucleic acid of interest and one or more additional active compounds.
  • a pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral, e.g., intravenous, intradermal,, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Intravenous administration is preferred.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF; Parsippany, NJ) or phosphate buffered saline (PBS).
  • the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, -polyalcohols such as mannitol, sorbitol, sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compound (e.g., a polypeptide or antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed.
  • compositions can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
  • a binder such as microcrystalline cellulose, gum tragacanth or gelatin
  • an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch
  • a lubricant such as magnesium stearate or Sterotes
  • a glidant such as colloidal silicon dioxide
  • a sweetening agent such as sucrose or saccharin
  • the compounds are delivered in the form of an aerosol spray from a pressurized container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
  • a suitable propellant e.g., a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
  • the compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
  • suppositories e.g., with conventional suppository bases such as cocoa butter and other glycerides
  • retention enemas for rectal delivery.
  • the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art.
  • the materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811 .
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the individual to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
  • the preferred dosage is 0.1 mg/kg to 100 mg/kg of body weight (more preferably, 0.1 to 20 mg/kg, 0.1-10 mg/kg).
  • body weight more preferably, 0.1 to 20 mg/kg, 0.1-10 mg/kg.
  • partially human antibodies and fully human antibodies have a longer half-life within the human body than other antibodies. Accordingly, lower dosages and less frequent administration is often possible.
  • Modifications such as lipidation can be used to stabilize antibodies and to enhance uptake and tissue penetration (e.g., into the gastrointestinal system).
  • a method for lipidation of antibodies is described by Cruikshank et al. (1997, J. Acquired Immune Deficiency Syndromes and Human Retrovirology 14:193 ).
  • an effective amount of protein or polypeptide ranges from about 0.001 to 30 mg/kg body weight, preferably about 0.01 to 25 mg/kg body weight, more preferably about 0.1 to 20 mg/kg body weight, and even more preferably about 0.1 to 1.0 mg/kg, 1 to 10 mg/kg, 2 to 9 mg/kg, 3 to 8 mg/kg, 4 to 7 mg/kg, or 5 to 6 mg/kg body weight.
  • treatment of a individual with a therapeutically effective amount of a protein, polypeptide, or antibody can include a single treatment or, preferably, can include a series of treatments.
  • the present invention encompasses the use of small molecules that modulate expression or activity of a nucleic acid or polypeptide of interest.
  • small molecules include peptides, peptidomimetics, amino acids, amino acid analogs, polynucleotides, polynucleotide analogs, nucleotides, nucleotide analogs, organic or inorganic compounds ( i.e,.
  • a microarray or QRT-PCR kit may be produced for detecting one or more colon pathologies including polyps or one or more subtypes of polyps and contain only those reagents and materials necessary for measuring the levels of RNA products of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, or all or any combination of the biomarkers of the invention.
  • the kits can comprise materials and reagents that are not limited to those required to measure the levels of RNA products of 1,2, 3, 4, 5, 6, 7, 8 or all or any combination of the biomarkers of the invention.
  • a microarray kit may contain reagents and materials necessary for measuring the levels of RNA products not necessarily associated with or indicative of one or more colorectal pathologies , in addition to reagents and materials necessary for measuring the levels of the RNA products of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, or all or any combination of the biomarkers of the invention.
  • a microarray or QRT-PCR kit contains reagents and materials necessary for measuring the levels of RNA products of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, or all or any combination of the biomarkers of the invention, and 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 300, 350, 400, 450, or more genes other than the biomarkers of the invention, or 1-10, 1-100, 1-150, 1-200, 1-300, 1-400, 1-500, 1-1000, 25-100, 25-200, 25-300, 25-400, 25-500, 25-1000, 100-150, 100-200, 100-300, 100-400, 100-500, 100-1000, 500-1000 other genes than the biomarkers of the invention.
  • the kits generally comprise probes attached or localized to a support surface.
  • the probes may be labeled with a detectable label.
  • the probes are specific for an exon(s), an intron(s), an exon junction(s), or an exon-intron junction(s)), of RNA products of 1, 2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention.
  • the microarray kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.
  • the kits comprise instructions for detecting or diagnosing one or more colorectal pathologies including one or more polyps or one or more subtypes of polyps.
  • kits may also comprise hybridization reagents and/or reagents necessary for detecting a signal produced when a probe hybridizes to a target nucleic acid sequence.
  • the materials and reagents for the microarray kits are in one or more containers. Each component of the kit is generally in its own a suitable container.
  • the kit also includes a computer readable medium which has a formula which uses data representing a level of products of at least one biomarker and generating an indication of the probability that a test subject has one or more colorectal pathologies or a subtype of colorectal pathology including a polyp or one or more subtypes of polyps.
  • the formula of the computer-readable medium can be generated by using the methods outlined in section (G).
  • the kits generally comprise pre-selected primers specific for particular RNA products (e.g., an exon(s), an intron(s), an exon junction(s), and an exon-intron junction(s)) of 1, 2, 3, 4, 5, 6, 7, 8, or all or any combination of the biomarkers of the invention.
  • the QRT-PCR kits may also comprise enzymes suitable for reverse transcribing and/or amplifying nucleic acids (e.g., polymerases such as Taq), and deoxynucleotides and buffers needed for the reaction mixture for reverse transcription and amplification.
  • the QRT-PCR kits may also comprise probes specific for RNA products of 1,2, 3, 4, 5, 6, 7, 8, or all or any combination of the biomarkers of the invention.
  • the probes may or may not be labeled with a detectable label (e.g., a fluorescent label).
  • a detectable label e.g., a fluorescent label.
  • Each component of the QRT-PCR kit is generally in its own suitable container.
  • the kit also includes a computer readable medium which has a formula which uses data representing a level of products of at least one biomarker and generating an indication of the probability that a test subject has one or more colorectal pathologies or a subtype of colorectal pathology including a polyp or one or more subtypes of polyps.
  • the formula of the computer-readable medium can be generated by using the methods outlined in section (G).
  • kits generally comprise distinct containers suitable for each individual reagent, enzyme, primer and probe.
  • the QRT-PCR kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.
  • the kits contain instructions for diagnosing or detecting one or more colorectal pathologies including one or more polyps or one or more subtypes of polyps.
  • the kit is a QRT-PCR kit.
  • a kit may comprise a 96 well plate and reagents and materials necessary for SYBR Green detection.
  • the kit may comprise reagents and materials so that beta-actin can be used to normalize the results.
  • the kit may also comprise controls such as water, phospate buffered saline, and phage MS2 RNA.
  • the kit may comprise instructions for performing the assay and methods for interpreting and analyzing the date resulting from the performance of the assay.
  • the instructions state that the level of a RNA products of 1, 2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention should be examined at two concentrations that differ by, e.g., 5 fold to 10-fold.
  • the kit can comprise, for example: (1) a first antibody (which may or may not be attached to a support) which binds to protein of interest (e.g., a protein products of 1, 2, 3, 4, 5, 6, 7, 8, all or any combination of the biomarkers of the invention); and, optionally, (2) a second, different antibody which binds to either the protein, or the first antibody and is conjugated to a detectable label (e.g., a fluorescent label, radioactive isotope or enzyme).
  • the antibody-based kits may also comprise beads for conducting an immunoprecipitation. Each component of the antibody-based kits is generally in its own suitable container. Thus, these kits generally comprise distinct containers suitable for each antibody.
  • kits may comprise instructions for performing the assay and methods for interpreting and analyzing the data resulting from the performance of the assay.
  • the kits contain instructions for diagnosing or detecting one or more colorectal pathologies including one or more polyps or one or more subtypes of polyps.
  • the kit contains instructions for applying the data to a formula in the form of a computer readable medium which contains said instructions. Said computer readable medium can also contain instructions for interpreting the analyzing the data resulting from the performance of the assay.
  • SNP Single Nucleotide Polymorphism
  • SNPs are a single nucleotide variation at a specific location in the genome of different individuals. SNPs are found in both coding and non-coding regions of genomic DNA. In spite of the paucity of scorable phenotypes, SNPs are found in large numbers throughout the human genome ( Cooper et al., Hum Genet 69:201-205, 1985 ). SNPs are stable genetic variations frequently found in genes, and contribute to the wide range of phenotypic variations found in organisms. Single nucleotide polymorphisms (SNPs) can be of predictive value in identifying many genetic diseases, as well as phenotypic characteristics. It is known for example that certain SNPs result in disease-causing mutations such as the SNP correlated with heritable breast cancer ( Cannon-Albright and Skolnick, Semin. Oncol. 23:1-5, 1996 ).
  • the instant invention offers a more focused and efficient method of screening SNPs to identify those SNPs which are specifically associated with one or more colorectal pathologies by having identified a selection of genes which are differentially expressed in blood from individuals having one or more colorectal pathologies as compared with individuals not having said one or more colorectal pathologies.
  • a selection of SNPs to be screened are those SNPs found in the genes listed in Tables 2 and 6.
  • novel SNPs can be identified in the disease-associated biomarkers using those methods listed above.
  • a SNP is considered to be a polyp associated SNP, if those individuals having one or more colorectal pathologies have a different polymorphism at the SNP locus than those individuals not having the one or more colorectal pathologies.
  • a particular SNP is considered to be diagnostic for one or more colorectal pathologies if a particular polymorphism of the SNP is found to present at a statistically significant higher frequency in those individuals having one or more colorectal pathologies than in those individuals not having the one or more colorectal pathologies. Indices of statistical significance include p ⁇ 0.05, p ⁇ .001, p ⁇ 01, and p ⁇ .10. This invention includes methods of determining the diagnostic value of SNPs with respect to diagnosing or detecting one or more colorectal pathologies.
  • a preferred sample is blood, but these methods encompass any samples from which DNA can be obtained including epithelial cells, buccal cells, hair, saliva, tissue cells and the like.
  • tissue and/or blood samples There are a variety of available methods for obtaining and storing tissue and/or blood samples. These alternatives allow tissue and blood samples to be stored and transported in a form suitable for the recovery of genomic DNA from the samples for genotype analysis.
  • DNA samples can be collected and stored on a variety of solid mediums, including Whatmann paper, Guthrie cards, tubes, swabs, filter paper, slides, or other containers. When whole blood is collected on filter paper, for example, it can be dried and stored at room temperature.
  • the blood sample may be any one of various types of blood samples, including, for example, a sample of serum-depleted blood, a sample of erythrocyte-depleted blood, a sample of serum-depleted and erythrocyte-depleted blood, a sample of lysed blood, a blood sample which has not been fractionated into cell types and a sample of unfractionated cells of a lysed blood sample. Examples of blood samples are described in Example 1 of the Examples section below.
  • polyp associated SNPs can be identified from RNA transcripts of the polyp biomarker genes, listed in Tables 2 and 6, instead of from genomic DNA.
  • RNA is isolated from a sample such as blood, from individuals with and without the given disease or disorder, and transcripts encoded by these polyp biomarker genes are reversed transcribed into cDNA.
  • the cDNA is amplified and analyzed to determine the presence of SNPs in the polyp biomarker genes.
  • a polyp associated SNP can be identified by then comparing the distribution of each of the SNPs identified in the polyp associated biomarker gene(s) differentially expressed in those individuals having one or more colorectal pathologies and individuals who do not have one or more colorectal pathologies.
  • the RNA transcripts of the disease specific biomarker genes, or their amplified products are analyzed for the presence of SNPs.
  • Analysis of genomic DNA comprising the polyp biomarker genes has the potential to identify SNPs in the coding region as well as in regulatory regions, the latter which may contribute to the change in expression levels of the gene.
  • Analysis of cDNA encoded SNPs has the potential to identify only SNPs in the coding region of the polyp biomarker genes, which may be instrumental in deciphering protein based mechanisms of polyp formation.
  • Methods of analyzing cDNA encoded SNPs can be carried out by analyzing the cDNA generated in the reverse transcription PCR reactions described herein that are used to identify the level of the biomarker in samples from patients and non patients.
  • a polyp associated SNP may be identified in the DNA of the polyp biomarker genes by a number of methods well known to those of skill in the art (see for example U.S. Pat. Nos. 6,221,592 and 5,679,524 ), including but not limited to identifying the SNP by PCR or DNA amplification, Oligonucleotide Ligation Assay (OLA) ( Landegren et al., Science 241:1077, 1988 ), Doublecode OLA, mismatch hybridization, mass spectrometry, Single Base Extension Assay, ( US6,638,722 ), RFLP detection based on allele-specific restriction-endonuclease cleavage ( Kan and Dozy, Lancet ii: 910-912, 1978 ), hybridization with allele-specific oligonucleotide probes ( Wallace et al., Nucl Acids Res 6:3543-3557, 1978 ), including immobilized oligonucleotides ( Saiki et al.,
  • thermostable polymerases of OmniBase Sequencing Enzyme, Pfu DNA Polymerase,Taq DNA Polymerase, Taq DNA Polymerase, Sequencing Grade, TaqBead Hot Start Polymerase, AmpliTaq Gold, Vent DNA Polymerase, Tub DNA Polymerase, TaqPlus DNA Polymerase, Tfl DNA Polymerase, Tli DNA Polymerase, Tth DNA Polymerase; the DNA Polymerases of DNA Polymerase I, Klenow Fragment, Exonuclease Minus, DNA Polymerase I, DNA Polymerase I Large (Klenow) Fragment, Terminal Deoxynucleotidyl Transferase, T7 DNA Polymerase, T4 DNA Polymerase
  • Recognition moieties incorporated into primers, incorporated into the amplified product during amplification, or attached to probes are useful in the identification of the amplified molecules.
  • a number of different labels may be used for this purpose such as, for example: fluorophores, chromophores, radio-isotopes, enzymatic tags, antibodies, chemiluminescence, electroluminescence, affinity labels, etc.
  • affinity labels include but are not limited to the following: an antibody, an antibody fragment, a receptor protein, a hormone, biotin, DNP, or any polypeptide/protein molecule that binds to an affinity label and may be used for separation of the amplified gene.
  • enzyme tags include enzymes such as urease, alkaline phosphatase, or peroxidase.
  • colorimetric indicator substrates can be employed to provide a detection means visible to the human eye or spectrophotometrically, to identify specific hybridization with complementary nucleic acid-containing samples. All these examples are generally known in the art and the skilled artisan will recognize that the present disclosure is not limited to the examples described above.
  • fluorophores are specifically contemplated to be useful in the present disclosure: Alexa 350, Alexa 430, AMCA, BODIPY 630/650, BODIPY 650/665, BODIPY-FL, BODIPY-R6G, BODIPY-TMR, BODIPY-TRX, Cascade Blue, Cy2, Cy3, Cy5, 6-FAM, Fluorescein, HEX, 6-JOE, Oregon Green 488, Oregon Green 500, Oregon Green 514, Pacific Blue, REG, Rhodamine Green, Rhodamine Red, ROX, TAMRA, TET, Tetramethylrhodamine, and Texas Red.
  • the DNA amplification products of the disclosed methods may be analyzed using DNA chips or microarrays in order to detect SNPs.
  • the amplified DNA products may then be passed over a DNA chip or microarray encompassing oligonucleotide or polynucleotide probes.
  • the ability or inability of the amplified DNA to hybridize to the microarray or DNA chip will facilitate the characterization of the SNPs present in the biomiarker genes encoding the transcripts present in the sample.
  • RNA quality was assessed on Agilent 2100 Bioanalyzer RNA 6000 Nano Chips as specified by the manufacturer, and RNA quantity was determined by absorbance at 260 nm in a Beckman-Coulter DU640 Spectrophotometer.
  • Lysis Buffer is added directly to the blood sample (where the blood sample does not have the serum removed) in a ratio of 3 parts Lysis Buffer to 1 part blood (Lysis Buffer (1L) 0.6g EDTA; 1.0g KHCO2, 8.2g NH4C1 adjusted to pH 7.4 (using NaOH)).
  • Lysis Buffer (1L) 0.6g EDTA; 1.0g KHCO2, 8.2g NH4C1 adjusted to pH 7.4 (using NaOH)
  • Sample is mixed and placed on ice for 5-10 minutes until transparent. Lysed sample is centrifuged at 1000 rpm for 10 minutes at 4°C, and supernatant is aspirated. Pellet is resuspended in 5ml Lysis Buffer, and centrifuged again at 1000 rpm for 10 minutes at 4°C.
  • the ratios used to generate the matrix of ⁇ Cts was further constrained by requiring each ratio to be comprised of one upregulated gene and a second downregulated gene where the ⁇ Ct was generated by subtracting the Ct of the downregulated gene from the Ct of the upregulated gene.
  • MBTPS 1, MGC45871, MKLN1, NIPBL were identified as upregulated genes (ie when comparing polyps vs non polyp individuals) ( FIG. 3 ) .
  • APEH, MGC40157, PPP1R2, FLJ23091 were identified as down regulated genes ( FIG. 3 ) .
  • the advantages of gene-pair ratio method include a) reducing inter-individual variability, b) permitting analysis of individual samples without references so as to ensure technical differences between plates are minimized, c) can use any reliable method (microarray, real-time PCR, etc), d) independent of the platform utilized for data acquisition, e) no housekeeping gene required (relatively independent of the input of sample amount), f) translating the strengths of micorarray expression profiling into simple clinical tests, g) highly precise in disease discrimination.
  • a reference (training) data set (AJ36h) was constructed containing ⁇ Ct values for each possible ratio as described and constrained as noted above for the above eight genes assayed against a total of 178 subjects including 110 subject without pathology (Female/male: 55/54 with one missing information, age average 57 year ranging 23 to 83 years of age) and 68 subjects with diagnosed colorectal pathology Female/male: 22/45 with one missing information, age average 57 ranging from 38 to 82 years).
  • the types of pathology identified include 21 (31%) tubular adenomas, 18 (27%) hyperplastic and 7 (10%) high risk pathology (villous morphology) and 22 (32%) other minor polyp (see Table 7 ).
  • a blind set of 80 clinical samples were tested.
  • the test set consisted of 40 controls and 40 subjects with one or more colorectal pathologies (having one or more polyps of any type). None of the test subjects used in the blind test were used to generate a classifier for each possible combination of the ratio of biomarkers "ratios" where each ratio is selected as a combination of an upregulated gene (when comparing colorectal pathology to no colorectal pathology) and a down regulated gene (when comparing colorectal pathology to no colorectal pathology).
  • MBTPS1, MGC45871, MKLN1, NIPBL were identified as upregulated genes (ie when comparing polyps vs non polyp individuals ( FIG. 3 ) .
  • APEH, MGC40157, PPP1R2, FLJ23091 were identified as down regulated genes ( FIG. 3 ) .
  • LIM domain containing preferred translocation partner in lipoma LIM domain containing preferred translocation partner in lipoma (LPP) Gene ID 4026; cytidine deaminase (CDA) Gene ID 978; sarcoma antigen NY-SAR-48 (MCG20553) Gene ID 93323; serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 (SERPINE 2) Gene ID 5270; B-cell novel protein 1 (BCNP1) Gene ID 199786; hypothetical protein MGC45871 (MGC45871) Gene ID 359845; membrane-bound transcription factor protease, site 1 (MBTPS1) Gene ID 8720. Genes were chosen from either Table 1 or other similar experiments.
  • a reference (training) data set was constructed containing ⁇ Ct values for the above seven genes assayed against a total of 185 subjects having any type of polyp and 239 subjects not having polyps.
  • a reference (training) data set was constructed containing ⁇ Ct values for the above seven genes assayed against a total of 252 subjects having high risk polyps and 272 subjects having other types of polyps or having no pathology where by high risk polyps is meant Tubulovillous Adenoma, Villous Adenoma, High Grade Dysplasia and Tubular Adenoma - regardless of diameter of polyp.
  • Biomarkers to screen for presence of colorectal cancer Deriving classifiers to be used with combinations of biomarkers and application of said classifiers to determine presence of colorectal cancer
  • QRT-PCR was performed on a selection of the genes identified from one or more microarray analyses (data not shown) as being able to differentiate as between individuals having colorectal cancer and individuals not having colorectal cancer. Some of genes selected for QRT-PCR were selected from microarray data performed on samples collected from three regions of China for over 593 samples including 61 samples from individuals having been diagnosed with colorectal cancer and 532 from individuals not having colorectal cancer (data not shown). Other genes were selected from other similar microarray experiments with individuals from North America and/or Asia. Among the individuals not having colorectal cancer was a mixture of individuals having breast cancer, kidney cancer, prostate cancer, bladder cancer, and individuals having other subtypes of colorectal pathology which were not colorectal cancer.
  • QRT-PCR was done on each individual gene across a population of individuals having colorectal cancer and a population of individuals not having colorectal cancer.
  • QRT-PCR experiments were done using either the SYBR® Green Kit from Qiagen (Product Number 204143) and/or using Applied Biosystems PCR reagent kits (Cat 4334973) and/or using TaqMan Assay using the QuantiTect® Probe PCR Kit (Qiagen, Cat. # 204345).
  • TaqMan® probes were developed for each gene of interest and labelled with FAM and the Black Hole Quencher® from Biosearch Technologies.
  • Beta-actin was used as a housekeeping gene in the duplexed assays and labelled using HEX and Black Hole Quencher®. Amplicons were detected in real time using a Prism 7500 instrument (Applied Biosystems). Results of the QRT-PCR for each gene across the population tested are shown in Table 12.
  • all possible combinations of biomarkers with a p value of less than 0.05 can be chosen and all or a portion of combinations of biomarkers tested. Discussed below is representative classifiers identified for selected combinations tested.
  • Classifiers were derived for all two gene combinations of the biomarkers identified in Table 12 using QRT-PCR for 28 of the genes identified in Table 12 across 58 individuals having colorectal cancer and 57 individuals not having colorectal cancer.
  • the 28 genes utilized are represented by the following gene symbols and are described in more detail herein: OSBPL10, LOC283130, BANK1, COBLL1, MGC24039, C9orf85, BLNK, BCNP1, PDE3B, AKAP13, WDFY1, CDA, AGTRAP, ACTR2, UTS2, MS4A1, SPAY1, ANK3, KIAA1559, GBP5, MGC20553, CEACAM1, HISTIH4H, PRG1, BRD2, LTBP3, MAP4K3, and NIPA2 Primers utilized for the real time RT-PCR are further described in Table 16.
  • ROC area is provided in addition to the specificity (when sensitivity is set at 90%) and sensitivity (when specificity is set at 90%).
  • the cutoff utilized to generate the sensitivity and specificity as noted are provided in the two righthand most columns.
  • Classifiers are chosen depending on the specific sensitivity and specificity requirements of the specific intended use of the biomarkers (for example, if may be desirable to have a high sensitivity and fewer false negatives so as to miss less colorectal cancers); (alternatively high specificity resulting in lower false positives is also desirable as it can decrease costs of additional unnecessary medical interventions).
  • a blind test is conducted on one or more of the resulting classifiers so as to demonstrate the utility of the classifier to test for colorectal cancer in a test individual.
  • One or more the classifiers is applied to test an individual to determine the likelihood of said test subject having colorectal cancer.
  • the reference (training) data set was constructed containing ⁇ Ct values for the above five genes assayed against a total of 57 subjects having colorectal cancer and 58 subjects not having colorectal cancer as described in more detail in Example 7.
  • a first blind test was performed using a scoring population comprised of 15 individuals not having colorectal cancer and 6 individuals having colorectal cancer. This blind test utilized individuals selected from a single site in Penang. The first blind test resulted in a sensitivity of 100% and a specificity of 43%.
  • a second blind test was performed using a second scoring population (non overlapping with the first scoring population) of 31 non colorectal patients and 23 colorectal patients. Patient samples were collected from three different sites in Asia. The test resulted in a sensitivity of 100% (all samples with colorectal cancer properly identified) and a specificity of 47% (almost half of the samples without colorectal cancer properly identified).
  • a final blind test was performed utilizing samples obtained from two clinics in North America including 15 colorectal cancer patients and 16 non colorectal cancer patients resulting in a sensitivity of 88% and a specificity of 33%.
  • QRT-PCR was performed on the selection of genes BCNP1, CD163, CDA, MS4A1, BANK1, MCG20553 identified from one or more microarray analyses (selected from Table 12 and Table 1 1).
  • QRT-PCR data was most recently collected on RNA samples from centrifuged lysed blood from 109 samples, 60 individuals having colorectal cancer and 59 individuals not having colorectal cancer.
  • QRT-PCR was performed using a duplexed TaqMan Assay using the QuantiTect® Probe PCR Kit (Qiagen, Cat. # 204345). TaqMan® probes were developed for each gene of interest and labelled with FAM and the Black Hole Quencher® from Biosearch Technologies. Beta-actin was used as a housekeeping gene in the duplexed assays and labelled using HEX and Black Hole Quencher®. ⁇ Cts (Ct gene of interest - Ct Beta-actin) were calculated.
  • Table D Each combination is noted as a unique combination number ranging from 1 to 63. Presence of the number 1 in a column below a noted Gene indicates the presence of that gene within the generated classifier.
  • Table E Classifiers resulting from each possible combination of the six biomarkers are noted.
  • the Combination number corresponds to the combinations as noted in Table D.
  • the number of genes contributing to the combination is noted, and the coefficient for that biomarker are noted within the row. Where 0 is noted as a coefficient, this biomarker does not contribute to the resulting classifier.
  • the area under the curve (ROC area) is noted as is the sensitivity at 90% specificity and the specificity at 90% sensitivity.
  • a classifier is developed using each of the following methods (a) logistic regression, (b) linear regression (c) neural networks and (d) principle component analysis.
  • a formula consisting of each of the classifiers, wherein each classifier itself is given a weighting of equal value is generated (ie the results of each classifier when applied to a test subject will give an indication of whether the test subject has a colorectal pathology, and then the results of each classifier are tallied such that if, for example, 3 of the 4 classifiers indicate the test subject has colorectal pathology, the results of the formula indicate the test subject has colorectal pathology).
  • a blood sample is isolated from a test subject.
  • Total RNA from the blood sample is isolated and cDNA derived using an oligo dT primer.
  • QRT-PCR is performed in each of the six genes in the sample and a ⁇ Ct generated for each gene in reference to a Beta-actin control.
  • the data from the test subject's sample is input into the formula consisting of the four classifiers and a result of each classifier determined, along with the results of the sum of the four classifiers to provide an indication of whether said test subject has colorectal pathology, and in particular colorectal cancer.
  • FLJ14624 NM 032813 NP 116202 Homo sapiens hypothetical protein FLJ14G24 (FLJ14624), mRNA FLJ14624 NM 032813 NP 116202 Homo sapiens hypothetical protein FLJ14624 (FLJ14624), mRNA ETS 1 NM 005238 NP 005229 Homo sapiens v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) (BTS1), mRNA RPS24 NM 033022 NP 148982 Homo sapiens ribosomal protein S24 (RPS24), transcript variant 1, mRNA RPS24 NM.
  • FLJ14624 Protein Accession No. Description FLJ14624 NM 032813 NP 116202 Homo sapiens hypothetical protein FLJ14G24 (FLJ14624), mRNA FLJ14624 NM 032813 NP 116202 Homo sapiens hypothetical protein FLJ14624 (FLJ14624), mRNA ETS 1 NM
  • GUS beta-glucuronidase Hydrolyzes colorless glucuronides to yield colored products.
  • LUC luciferase Oxidizes luciferin, emitting photons GFP (green fluorescent protein) Fluorescent protein without substrate SEAP (secreted alkaline phosphatase) Luminescence reaction with suitable substrates or with substrates that generate chromophores HRP (horseradish peroxidase) In the presence of hydrogen oxide, oxidation of 3,3',5,5'-tetramethylbenzidine to form a colored complex AP (alkaline phosphatase) Luminescence reaction with suitable substrates or with substrates that generate chromophores
  • Other Family Antibodies Available including: Abcam Ab10346 AKAP12 AntiRat Rabbit Polyclonal Antibody Abcam Ab 25805 AKAP 9 AntiHuman Rabbit Polyclonal Antibody Abcam AB 14096 AKAP 3 Goat Polyclonal Antibody WDFY1 WD repeat and FYVE domain containing 1 (aka FENS-1) Abcam Ab21695 AntiHuman Goat Polyclonal Antibody CDA cytidine deaminase Abcam Ab5197 Antihuman Rabbit Polyclonal Antibody Duquette ML et al.
  • AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation.

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US20130013214A1 (en) 2013-01-10
CN102260742A (zh) 2011-11-30
CN101370946A (zh) 2009-02-18
EP1945816B1 (fr) 2011-07-27
AU2006304883A1 (en) 2007-04-26
CA2626604A1 (fr) 2007-04-26
JP2009512440A (ja) 2009-03-26
JP5237817B2 (ja) 2013-07-17
JP2013150612A (ja) 2013-08-08
ATE518007T1 (de) 2011-08-15
HK1128310A1 (en) 2009-10-23
US8239136B2 (en) 2012-08-07
AU2013205891A1 (en) 2013-06-06
US20150191796A1 (en) 2015-07-09
WO2007048074B1 (fr) 2007-06-28
EP1945816A1 (fr) 2008-07-23
CN101370946B (zh) 2011-07-20

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